Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Fixed
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Labels:None
Description
Open A. thal, RNA-seq> > > > SM> Graphs. Load both graphs. Select both, join (graphs tab>join).
notice the vertical zoom on the left is way down. If you scroll it up
to show everything, the three tracks are joined, but the refseq has very narrow
height.
Attachments
Issue Links
- relates to
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BUG-637 Graph >Join/Split bugs
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- Closed
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Activity
I can't get it to go in this example, but I have seen this a bunch - it is not very reproducible in this situation, but in general, IGB has been performing functions/adjustments to tracks and suddenly the data becomes too big for the main window size. Tracks get pushed below the main view window and can't be recovered, or the new data/new presentation of loaded tracks forces the vert zoom to increase, and forces data off the main view. See bug IGBC-333
If it does not reproduce in this case, I will close it. There already different bug for other cases.
Actually, load up as lance says, then individually change the colors of each graph via data adjuster tab - it reproduces what lance is complaining about.
Fixed in r12065.
The specified files from BUG-437 throw an error and user is prompted to remove the data from the list. Please provide new files or specify types of files (assuming they will be .wig files) to test bug.
Exception in Java Console
Dec 05, 2012 2:15:45 PM com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader logException
WARNING: For input string: "PUBLIC"
java.lang.NumberFormatException: For input string: "PUBLIC"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:492)
at java.lang.Integer.parseInt(Integer.java:527)
at com.affymetrix.genometryImpl.symloader.Wiggle.parseLines(Wiggle.java:616)
at com.affymetrix.genometryImpl.symloader.SymLoader.buildIndex(SymLoader.java:159)
at com.affymetrix.genometryImpl.symloader.Wiggle.init(Wiggle.java:90)
at com.affymetrix.genometryImpl.symloader.Wiggle.getChromosomeList(Wiggle.java:97)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.getChromosomeList(QuickLoadSymLoader.java:224)
at com.affymetrix.igb.view.load.GeneralLoadUtils$4.runInBackground(GeneralLoadUtils.java:1205)
at com.affymetrix.igb.view.load.GeneralLoadUtils$4.runInBackground(GeneralLoadUtils.java:1200)
at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:74)
at javax.swing.SwingWorker$1.call(SwingWorker.java:296)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at javax.swing.SwingWorker.run(SwingWorker.java:335)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:722)
You can use this files from BioViz (Das)
AtTile1R/GSE9646/10h_ABA/GSM243691
AtTile1R/GSE9646/10h_ABA/GSM243690
AtTile1R/GSE9646/10h_ABA/GSM243689
Passed V.13686, Mac, Java 1.7.0_09
Files that were previously referenced were downloaded and loaded into IGB properly.
After joining graphs, no issues to speak of. All tracks remain the same size, with the exception of the newly created 'Joined Graphs' track which encompasses the tracks of graphs that were joined.
Tested further with changing the colors individually for each separate track in the 'Joined Graphs' track to try to reproduce issue. No such issues.
Issue should be rewritten to account for new steps to reproduce
Cannot reproduce.