Also, the file will show and be checked under 'Local Files' in the 'Data Access' tab, but when unchecking the file another error is thrown in the console:

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadAndDisplayAnnotations(GeneralLoadUtils.java:710)
at com.affymetrix.igb.view.load.GeneralLoadView.loadFeature(GeneralLoadView.java:315)
at com.affymetrix.igb.view.load.GeneralLoadView.addFeature(GeneralLoadView.java:575)
at com.affymetrix.igb.view.load.FeatureTreeView$FeatureTreeCellEditor$FeatureLoadAction.actionPerformed(FeatureTreeView.java:688)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.JToggleButton$ToggleButtonModel.setPressed(Unknown Source)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at javax.swing.plaf.basic.BasicTreeUI$MouseInputHandler.mouseReleased(Unknown Source)
at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$000(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue$2.run(Unknown Source)
at java.awt.EventQueue$2.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)

I have fixed this npe. But it still won't show up in table.

fixed in r9962

OK... The attached "Arabidopsis.." CHP file is in legacy format, and now IGB pops up the window saying so. No errors, no problems. However, the attached second file "TisMap_brain..." chp file does not generate the 'legacy' pop-up window. It does throw an error:

java.lang.NullPointerException
at com.affymetrix.igb.featureloader.QuickLoad.addMethodsToFeature(QuickLoad.java:306)
at com.affymetrix.igb.featureloader.QuickLoad.loadAndAddAllSymmetries(QuickLoad.java:286)
at com.affymetrix.igb.featureloader.QuickLoad.access$000(QuickLoad.java:46)
at com.affymetrix.igb.featureloader.QuickLoad$1.runInBackground(QuickLoad.java:194)
at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:38)
at javax.swing.SwingWorker$1.call(SwingWorker.java:277)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at javax.swing.SwingWorker.run(SwingWorker.java:316)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:680)

Loads perfectly now on Mac. Katy please try on windows.

v10065 Windows

Loading attached "Arabidopsis..." shows pop up window "CHP file is in legacy format, cannot be loaded"

Loading attached "TisMap_brain..." shows pop up window "Couldn't find server to retrieve location data for CHP file, server = NetAffx"

No console errors/exceptions

The problem is that IGB takes a VERY long time to realize that the arabidopsis file is legacy, and when it pops up the error window, you can't immediately close it and finally, it pops up like 4 or 5 of these in a row.

Showed only one window to me.

how is this working for you? totally right, or multiple popup windows, or what?

Windows v11964

No console errors/exceptions

Loading attached "Arabidopsis..." shows ONE pop up window "CHP file is in legacy format, cannot be loaded"

Loading attached "TisMap_brain..." shows ONE pop up window "Couldn't find genome data on server for CHP file, genome = Unknown Genome 1"

I am still getting multiple popup windows (5 of them). The console log is attached... I know that my Java is up to date (although this might be one of those 'Alyssa only' bugs. But try running from webstart and see if that is the issue?

Program ID: GeneChipAnalysis.GEBaseCall.1
number of probesets: 22810
Stopped loading, parsing Legacy CHP data only partially implemented!

-------------------------------------------------------
ERROR: CHP file is in legacy format, cannot be loaded
-------------------------------------------------------

Parsing CHP file: /var/folders/XG/XGHkYUt9Gu82T4cqiJhnxE+++TQ/Tmp/ArabidopsisATH1-121502.CHP.gz7850241402517407750.tmp
CHP file is for legacy data: affymetrix.fusion.chp.FusionCHPLegacyData@764e7c4
Alg name: ExpressionStat
Alg version: 5.0
Assay type: 0
Chip type: ATH1-121501
Rows: 712, Columns: 712
Parent .cel file: ArabidopsisATH1-121502.CEL
Program ID: GeneChipAnalysis.GEBaseCall.1
number of probesets: 22810
Stopped loading, parsing Legacy CHP data only partially implemented!

-------------------------------------------------------
ERROR: CHP file is in legacy format, cannot be loaded
-------------------------------------------------------

Parsing CHP file: /var/folders/XG/XGHkYUt9Gu82T4cqiJhnxE+++TQ/Tmp/ArabidopsisATH1-121502.CHP.gz3588064759050536868.tmp
CHP file is for legacy data: affymetrix.fusion.chp.FusionCHPLegacyData@126536ee
Alg name: ExpressionStat
Alg version: 5.0
Assay type: 0
Chip type: ATH1-121501
Rows: 712, Columns: 712
Parent .cel file: ArabidopsisATH1-121502.CEL
Program ID: GeneChipAnalysis.GEBaseCall.1
number of probesets: 22810
Stopped loading, parsing Legacy CHP data only partially implemented!

-------------------------------------------------------
ERROR: CHP file is in legacy format, cannot be loaded
-------------------------------------------------------

Parsing CHP file: /var/folders/XG/XGHkYUt9Gu82T4cqiJhnxE+++TQ/Tmp/ArabidopsisATH1-121502.CHP.gz6279140797501919359.tmp
CHP file is for legacy data: affymetrix.fusion.chp.FusionCHPLegacyData@589f42c8
Alg name: ExpressionStat
Alg version: 5.0
Assay type: 0
Chip type: ATH1-121501
Rows: 712, Columns: 712
Parent .cel file: ArabidopsisATH1-121502.CEL
Program ID: GeneChipAnalysis.GEBaseCall.1
number of probesets: 22810
Stopped loading, parsing Legacy CHP data only partially implemented!

-------------------------------------------------------
ERROR: CHP file is in legacy format, cannot be loaded
-------------------------------------------------------

Parsing CHP file: /var/folders/XG/XGHkYUt9Gu82T4cqiJhnxE+++TQ/Tmp/ArabidopsisATH1-121502.CHP.gz4901623179079393163.tmp
CHP file is for legacy data: affymetrix.fusion.chp.FusionCHPLegacyData@2567115
Alg name: ExpressionStat
Alg version: 5.0
Assay type: 0
Chip type: ATH1-121501
Rows: 712, Columns: 712
Parent .cel file: ArabidopsisATH1-121502.CEL
Program ID: GeneChipAnalysis.GEBaseCall.1
number of probesets: 22810
Stopped loading, parsing Legacy CHP data only partially implemented!

-------------------------------------------------------
ERROR: CHP file is in legacy format, cannot be loaded
-------------------------------------------------------

Still cannot reproduce.

well, then this is a weird error on my machine and I am going to put this bug to bed...

Passed V.13624, Mac, Java 1.06.0_37 as the output is concurrent with an IMPROVEMENT discussed in the resolution of BUG-275

For Arabidopsis CHP file, 2 windows appear with the first being an Error stating:
-------------------------------------------------------
ERROR: Couldn't find genome data on server for file, genome = Unknown Genome 2
-------------------------------------------------------
and the second being an option from IGB to remove the file since it is not able to load.

The TisMap_Brain_01_v1_WTGene1.rma-gene-default.chp.gz caused IGB to react in the same manner with an error window and the option to remove the file since it is not able to load.

The Java console displayed the following errors:

net.sf.samtools.FileTruncatedException: Premature end of file
at net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:359)
at net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:109)
at net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:234)
at java.io.BufferedInputStream.fill(BufferedInputStream.java:235)
at java.io.BufferedInputStream.read1(BufferedInputStream.java:275)
at java.io.BufferedInputStream.read(BufferedInputStream.java:334)
at java.io.FilterInputStream.read(FilterInputStream.java:107)
at com.affymetrix.genometryImpl.util.GeneralUtils.convertStreamToFile(GeneralUtils.java:189)
at com.affymetrix.genometryImpl.util.LocalUrlCacher.convertURIToFile(LocalUrlCacher.java:645)
at com.affymetrix.genometryImpl.util.LocalUrlCacher.convertURIToFile(LocalUrlCacher.java:606)
at com.affymetrix.igb.parsers.QuickLoadSymLoaderChp.getGenome(QuickLoadSymLoaderChp.java:66)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddAllSymmetries(QuickLoadSymLoader.java:158)
at com.affymetrix.igb.view.load.GeneralLoadUtils$5.runInBackground(GeneralLoadUtils.java:1414)
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)
Nov 28, 2012 3:39:17 PM com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader logException
WARNING: null
java.lang.NullPointerException
at com.affymetrix.igb.parsers.QuickLoadSymLoaderChp.getGenome(QuickLoadSymLoaderChp.java:67)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddAllSymmetries(QuickLoadSymLoader.java:158)
at com.affymetrix.igb.view.load.GeneralLoadUtils$5.runInBackground(GeneralLoadUtils.java:1414)
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)

Nov 28, 2012 3:39:17 PM com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader logException
WARNING: java.lang.NullPointerException
java.lang.RuntimeException: java.lang.NullPointerException
at com.affymetrix.igb.parsers.QuickLoadSymLoaderChp.getGenome(QuickLoadSymLoaderChp.java:72)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddAllSymmetries(QuickLoadSymLoader.java:158)
at com.affymetrix.igb.view.load.GeneralLoadUtils$5.runInBackground(GeneralLoadUtils.java:1414)
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)
Caused by: java.lang.NullPointerException
at com.affymetrix.igb.parsers.QuickLoadSymLoaderChp.getGenome(QuickLoadSymLoaderChp.java:67)
... 10 more

Hiral, this CHP used to work just fine. Has the CHP format been entirely set to 'legacy' status? Or is there a bug in the system?

CHP are genome specific and requires a active DAS2 server to load it properly.