Services to sum or subtract highlighted numbers and calculate equations

Years ago, I discovered the convenience of treating the Spotlight search as a calculator.  If you paste in an equation, the top result will be what the calculator app produces given the math you’ve typed or paste in.  I take a lot of notes in my work and frequently have a simple equation to calculate or numbers to sum or subtract.  It’s easy enough to copy and paste an equation into spotlight or paste a set of numbers (with some manual clean-up) to Excel or even search & replace with plus or minus signs & paste into spotlight, but you’d be surprised how much more efficient it feel to do this automatically.  You can even have it paste the result after the end of the highlight.

Combine this with the fact that many text editing apps allow you to select columns of text, and it becomes a trivial matter to do things with masses of numbers in any text and any app.

The sum & subtract automator services also conveniently strip out non-number characters, so you can highlight any numbers that have text in between and sum or subtract them.

Sum Service

Let’s start with the Sum service.  Here’s an example of how it works:

sum_demo.gif

As seen above, you simply:

  1. Select text with the numbers you want to sum
  2. Right-click the selection, and
  3. Select Services->Sum.

The numbers are parsed and added using Spotlight.  In the demo above, I simply tap the escape ket to exit spotlight after seeing the result.  But, you could select & copy the result to use it how you wish, directly from the spotlight result listing.

Subtract Service

The subtract service works the same way as the Sum Service above, but instead of adding all the numbers, it simply takes the first number and subtracts all the rest.  Both services ignore non-numbers and can handle decimals.  It even knows the difference between hyphens in words versus negative numbers.  However, they may have some trouble with non-standard hyphen characters and periods in full sentences.

Calculate (& Append Result) Service(s)

The Calculate Service (or “Calculate & Append Result”) will take any equation that Spotlight (i.e. the Calculator app) can handle and compute the result.  And if you know already that you will want to append the result after the highlighted text in the form of ” = answer”, you can alternatively select the “Calculate & Append Result” Service.  Here is a demo using the service:

calc_demo.gif

Installation

  1. Go to the github gist containing the Applescript code for each service
  2. Copy the code from one of the 3 files in the github gistcopygistcode.png
  3. Open Automator.appautomatordock.png
  4. Select service “Service”/gear icon from the dropdown sheet & click “Choose”selectservice.png
  5. Drag the “Run AppleScript” action into your workflowautomatorapplescript.gif
  6. Replace the purple code in the Run AppleScript action with the code you copied in step 1
  7. Save the workflow and name it however you would like it to appear in the services contextual menu (E.g. “Calculate & Append Result.workflow” – the extension will not appear in the menu)
  8. Repeat for the remaining 3 services.

The workflows/services will be saved automatically to your Library/Services directory in your home directory.  If you right-click the file name at the top of the window in Automator, you can select the Services folder to reveal it in the Finder.  You can then copy that file and send it to any other computer you would like to also have that service.

Have fun!

Disclaimers: These services are only intended as a quick and dirty solution to work in any context, & any app.  If you have a repeated common use-case, consider other solutions.  Note also that any application which reserves the arrow keys for some function when the shift key is held down, other than modifying the most recent selection, this service will fail.  Some applications, such as java applications, modify selections using shift-arrow navigation differently, depending on the direction of the mouse drag during text selection.  This can produce unexpected results.  A work-around for both such issues can be to use the strategy used for Terminal.app, but this would required modification to the code.  A few of the features in the script rely on some tricks such as statically set delays and command-line calls, necessary to either wait for an application to respond or to control the focus of various windows.  If your computer is very busy or has any configuration issues, the proper functioning of these services may be disrupted.  These services were developed and tested on macOS High Sierra, 10.13.4.  They may or may not work in other macOS versions.

Advertisements

Automator Services for finding coordinates in DNA/AA strings

Do you write code to analyze or modify DNA or proteins?  Do you do your work on a Mac?  If so, I have a few Automator Services, written in AppleScript, that you may find very handy:

  1. Get the sequence (& alignment) length of a selected nucleotide string
  2. Get the sequence length of any selected string (e.g. protein or quality string)
  3. Show where a coordinate is in any selected string (including white-spaces)
  4. Show where a coordinate is in a selected sequence (e.g. protein or quality string)
  5. Show where a nucleotide coordinate is in a selected sequence
  6. Show where an alignment coordinate is in a selected nucleotide sequence
  7. Get the reverse complement of a selected nucleotide sequence
  8. Guess the barcodes present in a FastQ file *NEW

With these, you can highlight a sequence anywhere in any application and either get the selection length or show where a supplied coordinate is in the selected sequence.

Each service, once installed, will show up in the contextual menu that shows up anytime you right-click any selected text, system-wide on your mac, under the services sub-menu, e.g.:

countntsservicemenu.png

Here are the full details of how to use each service and what it does:

1. Get the sequence (& alignment) length of a selected nucleotide string

Name: Count Nucleotides

countntsoutput.png

This service does a bit more than count nucleotides.  As seen in the example on the right, it reports the number of nucleotides in the selection (sequence length), the length of the selected alignment, the number of discrete & ambiguous nucleotides, and a breakdown of all case-insensitive sequence characters (including gaps and ambiguous nucleotides).

Spaces, tabs, newlines, carriage returns, numbers, or any other non-sequence characters are completely ignored, so you can select any sequence, even if it is formatted & displayed with coordinates.  Only the sequence found inside the highlighted text is considered.  The first selected sequence character is coordinate 1.

2. Get the sequence length of any selected string (e.g. protein or quality string)

Name: Count Sequence Characterscountnonwschars.png

This service counts every character selected except for spaces, tabs, newlines, and carriage returns.  It’s good for getting the length of selected unaligned protein sequences (with no formatted coordinates in the selection) or of quality strings.  Note, there is currently no service for aligned amino acid sequences, but if you would like such a service, let me know in the comments and I’ll whip one up.  I work mostly with DNA, thus I haven’t had much need for aligned protein coordinate determinations.

3. Show where a coordinate is in any selected string (including white-spaces)

Name: Select N Characters

This service works only on “solid sequence” (i.e. having no whitespaces, hard returns, or for that matter: any non-sequence characters).  See services 4-6 for sequence-specific functions.  The way this service shows where a coordinate is, is by changing the length of the selection.  The resulting last character of the selection after the length modification is the length supplied by you, the user.  For example, if you tell it to select 4 characters in this string you selected: ATGCCGTAG, the selection will end up as: ATGCCGTAG.

lengthprompt.png

There are 2 ways to supply the coordinate.  The default way is to grab the coordinate from the clipboard, so all you have to do is copy the number you want to use to set the selection length.  However, if the content of the clipboard is not a number, a popup window will appear to ask you to enter the desired selection length.

 

To use this service:

  1. [Optional] Copy a number/length indicating the amount of the sequence you want to select.
  2. Select any length of sequence from the start position (position 1)
  3. Right-click the selection and select Services -> Select N Characters
  4. [If you didn’t do step 1] Enter the length of sequence you want to select

This script alters the selection length of the selected text you right-clicked on in the window in which you clicked on the sequence, regardless of application.  However, if you are in Terminal.app, it displays the selection result in a popup window instead of in the Terminal itself.  This is because the modification of the selection length is accomplished by shift-arrow keystroke emulation and this is not a means by which you can modify a selection in the Terminal app.  This has 1 side effect.  Normally, if the entered length is longer than the selection, in any other app, that’s not a problem and the selection just expands, but in Terminal’s popup result window, all the service has access to is the selected text, so placeholder ‘N’s are appended to show the desired sequence length.

lengthresult-terminal.pngThere are other drawbacks to this Terminal selection-length work-around.  The font is not fixed-width and the width of the popup window is fixed at a fairly narrow size, thus large sequences cannot be displayed very well.

Since the selection modification happens via emulated keystrokes, it takes a little time for the final selection to be made, but you’ll see how fast it goes as you watch the selection being made.  Since it’s not instantaneous, the script will either adjust the selection from the end or select anew from the beginning for efficiency.

4-8. New services

Names: Select N Sequence Characters, Select N Nucleotides, Select N Alignment Characters, Reverse Complement, & Guess barcodes

These services operate just like Select N Characters, but take the character type into account.

Select N Sequence Characters doesn’t include whitespace characters such as spaces, tabs, and newlines in the calculation of a coordinate in a string.

Select N Nucleotides doesn’t include non-nucleotide characters such as white spaces, gap characters, numbers, etc. in the calculation of a coordinate in a string.

Select N Alignment Characters behaves just like Select N Nucleotides but includes gap characters in the calculation of a coordinate in a string as the one exception.

Guess Barcodes allows you to right-click on a file and find out what the likely barcodes are.  It takes a little bit to run and makes some common assumptions, but if you think the results are wrong, you are given the opportunity to tweak the parameters and run again.

Installation

  1. Go to the github gist containing the Applescript code for each service
  2. Copy the code from one of the 3 files in the github gistcopygistcode.png
  3. Open Automator.appautomatordock.png
  4. Select service “Service”/gear icon from the dropdown sheet & click “Choose”selectservice.png
  5. Drag the “Run AppleScript” action into your workflowautomatorapplescript.gif
  6. Replace the purple code in the Run AppleScript action with the code you copied in step 1
  7. Save the workflow and name it however you would like it to appear in the services contextual menu (E.g. “Count Non-Whitespace Characters.workflow” – the extension will not appear in the menu)
  8. Repeat for the remaining 6 services.

The workflows/services will be saved automatically to your Library/Services directory in your home directory.  If you right-click the file name at the top of the window in Automator, you can select the Services folder to reveal it in the Finder.  You can then copy that file and send it to any other computer you would like to also have that service.

Just try your new services out by right-clicking on selected text anywhere.selectncharsexample.gif

And as you can see from the example above, Select N Characters works on any text.

Have fun!

Disclaimers: These services are only intended as a quick and dirty solution to work in any context, & any app.  If you have a repeated common use-case, consider other solutions.  Note also that any application which reserves the arrow keys for some function when the shift key is held down, other than modifying the most recent selection, this service will fail.  Some applications, such as java applications, modify selections using shift-arrow navigation differently, depending on the direction of the mouse drag during text selection.  This can produce unexpected results.  A work-around for both such issues can be to use the strategy used for Terminal.app, but this would required modification to the code.  A few of the features in the script rely on some tricks such as statically set delays and command-line calls, necessary to either wait for an application to respond or to control the focus of various windows.  If your computer is very busy or has any configuration issues, the proper functioning of these services may be disrupted.  These services were developed and tested on macOS Sierra, 10.12.6.  They may or may not work in other macOS versions.

How to make Safari 10 auto-open specific file types

I’ve been annoyed for awhile now that Safari was auto-opening text files that I was trying to download in rapid succession via option-click on a series of links. The text documents kept popping up in front of my browser window and getting in the way.  Safari used to have preferences that you could set to tell it what to do with specific file types, but not anymore – at least not since Safari 10 on MacOS Sierra (10.12.x). The only options were to make Safari auto-open “safe” files or not auto-open any files at all. I was about to give up again.  I’ve tried to figure this out on multiple other occasions, but I’d finally had enough and decided to roll my own using Automator and some clever scripting… Continue reading

Turn On/Off Sighthound Security Cam Rules via IFTTT

We just moved, and in my last apartment, we lived on the second floor and I had my Foscam security camera [~$60] (which is controlled by the Basic version of Sighthound Video [$60]) trained on the only stairwell, which only captured people arriving or leaving. However in our new house, none of the doors are in locations where the camera only captures egress & ingress events.  There’s a bathroom right next to one door and the other is between the living room and the stairs.  Thus, anywhere I set up a security camera is bound to capture the regular activity inside the house. So I first experimented with setting the rules to make the cameras active during certain hours on the weekdays, which turned out pretty annoying, because my wife’s schedule is random.  What I needed was a way to turn the camera rules off & on based on when we arrive & leave the house, the same way I use WeMo to control the window unit air conditioners and the air filter.

I discovered that Sighthound has an IFTTT channel and an iOS app, but their IFTTT channel only has triggers upon motion detection and no “actions” that could be run using Life360 (the app I use to control the AC & filter – e.g. turn on when the first person arrives and off when the last leaves or vice versa).  So I emailed Sighthound to see if they had any tips for enabling and disabling camera rules.  They pointed me to one of their forums called Hacker’s Corner, where I got pointed in the right direction.

Here’s how to enable your security camera (rule) when the last person in your family leaves the house and disable the camera when the first person in your family arrives.

Continue reading

Arctic Blast Ice-Jam Warning System

Last winter, a house that I rent out sustained 11 thousand dollars worth of water damage because an ice jam formed above the gutters.  I learned a lot about how this happens during the ordeal.  Heat from the house melts the bottom layer of ice & snow on the roof.  The water from the melting trickles down the roof, but once it gets to the eaves (away from the heat because the eaves are not enclosed and extend away from the house), it freezes and forms a dam.  Since the water has nowhere to go, it backs up from the eaves between the roof and the ice above it and gets under the slates/shingles.

My tenants didn’t notice the water coming in in the dining room through the ceiling and walls until the damage had started showing on the first floor.  Once I was alerted, I hired a company to come and remove the ice dam above the gutters.

The conditions needed for an ice dam/jam to form on the roof are 4 or 5 days where the temperature never gets above freezing and ice or snow has accumulated on the roof.  Dealing with the ice jam was such an ordeal that this year, I wanted to figure out a way (or ways) to get an early warning that an ice jam could be forming.

I had an idea to use a moisture sensor in the windows that would sound an alarm if water made contact with the sensor.  There was one window in particular where the water built up the most, so I bought this cheap moisture sensor (only $12) and installed it between the window and the storm window:

moisturesensor

However, by the time it goes off, a good bit of damage will have occurred already.  That makes it a good backup, but I needed something predictive.  Long ago, I had tried looking into the possibility of getting weather alerts when the temperature stays below freezing for multiple days, however after installing tons of apps and even looking into IFTTT‘s weather channel, the best alerts I could find were when the temperature went below freezing on a single day.  So today I finally sat down and rolled my own way to get an alert after 4 or more days of freezing temperatures in a row.

The basic idea was, I wanted to use IFTTT‘s weather channel to add tomorrow’s high temperature from the forecast to a google spreadsheet every day.  I then would create a google script attached to the spreadsheet to email me when the last 4 entries in the spreadsheet all had values below 33 degrees (F).  The script can be set to be triggered whenever a new row is added.

The first hurdle I faced was that IFTTT only lets you set 1 location for weather alerts and I already have my location set to where I live (not where the house I rent out is) and I already have weather recipes that rely on my location (e.g. when the pollen count gets high, turn on my air filter).  If I was to change the location, all my recipes would use the new location, which made no sense.  So I posted to the reddit IFTTT board and found out from the suggestions there that you can create multiple IFTTT accounts connected to the same gmail address by using gmail’s magical “+” feature.  So if your gmail address is johndoe@gmail.com, you can register an alternate IFTTT account using johndoe+ifttt1@gmail.com.  Note, after you create the account, you’ll need to go into your account settings and change your default username from “johndoe+ifttt1” to something like “johndoeifttt1” because IFTTT complains about the plus sign.

Next, you must create an IFTTT recipe (now called an “Applet”).  The trigger will be the weather channel’s “tomorrow’s forecast” trigger and the action will be to add a row to a google drive spreadsheet.  The settings when you’re done should look like this:

temptospreadsheet.png

Note, you might need to add the Google Drive and WU Weather channels (now called “Services”) to your IFTTT account.  Make sure to go into the weather channel’s settings to ensure it’s set to the correct location and that you’ve given IFTTT‘s google drive channel permission to access your google drive.

Next, you’ll need to create a google drive folder named “IFTTT” (or whatever you entered in the recipe above).  In there, create a spreadsheet with the name you used for the IFTTT recipe.

You then need to add a script to the spreadsheet.  In the google docs tool bar, select “Tools->Script Editor…”.  Replace the code there with the following code, but be sure to enter your email address you want to receive the ice jam warnings.  Click the image to access copyable code on pastebin:

freezingmonitor.png

Save the script, click the “Select function” drop-down list, select the “createSpreadsheetChangeTrigger”, and click the play button.

You can now close the script editor window and test out your spreadsheet by entering temperatures in the first column.  I entered “22”, 4 times to test it out.  2 things should happen upon entering the 4th value:

  1. You receive the email alert
  2. Column 3 gets the value “ICE JAM WARNING!”

Now, when IFTTT adds a row, if it’s the fourth or more day in a row of freezing temperatures, you’ll get an email warning that maybe you should check for an ice jam!

Automatically create iOS reminders based on events added to a subscribed google calendar

My wife just got a new job which has an irregular schedule and long hours.  Unfortunately, I’d gotten accustomed to the fact that she always took care of feeding the cat and scooping her litter before I ever even thought about it.  Now, a few weeks into this new job, I’m getting myself in trouble when I forget to feed the cat or scoop the litter.  I imagine I’ll eventually get used to it, but until I do, I devised a clever way to get automatic reminders without me having to ask my wife her schedule every week and manually create the reminders, which means I’ll be less likely to forget.  Hopefully, I’ll start to get used to the routine and I’ll be able to delete this reminder scheme, but until then, here’s how I managed to do it.

Continue reading

Disable Pesky Facebook Calendar-App Notifications

internet_accounts

Internet accounts accessible via System Preferences are great.  Everyone’s on board.  E.g.:

internet_accounts2

You can create and maintain calendars in them and they all show up in your Calendar apps on your computer and on your mobile devices.  In most cases, you create events and you create alerts for those events and you get your notifications the way you want them. Except Facebook. Sure, Facebook gives you your events and your notifications… and it even shows you events you’ve been invited to: great! What’s not so great? Your friends can create alerts on their events – events you have no intention of ever going to – events halfway across the world – and those alerts trigger on all your devices as if you created the event and set up the alert notification. Other internet accounts, like Google, draw the distinction between your events and events in others’ calendars you’re subscribed to, but did not create yourself.  There are settings in your Calendar app that allow you to ignore alerts from these subscribed calendars.  You can even choose to ignore alerts from subscribed calendars in your Facebook account’s calendar sync, but it doesn’t do anything because don’t forget, facebook adds your friends’ events to your calendar as if you created them. You’re ignoring nothing. You cannot stop the Facebook calendar notifications without turning off all notifications from every calendar in your Calendar app.

So you go about your day and your calendar alert goes off. You take a quick look and get confused about a meeting without a marked location. Then you start digging and find out it’s some event half way across the country about some distant acquaintance’s pub crawl that you got mass invited to. Then you start seeing these notifications all the time! Pretty soon, you stop looking at the alerts and you miss the reminder for your meeting that you scheduled! So annoying.

Being able to see what’s going on via Facebook events in your Calendar app is convenient when you’re looking for something to do in the context of your own schedule, so you hate to delete the Facebook calendar subscription. Luckily, I found a way to stop those pesky alerts, but still be able to see Facebook events in your Calendar app.  Here’s how it works:

Continue reading