Merge pull request #237 from sanger-pathogens/v17_patch_branch

V17 patch branch

ChangeLog

@@ -9,7 +9,7 @@ Version 17
 		4) Upgraded Apache Commons Net jar - used for ftp'ing. 
 		5) Added Cram file loading and fixed defects around that code area (also related RT ticket #560982: Artemis fails to build from source).
 		6) Added display of bam secondary & supplementary alignment flags to read details pop-up window.
-		7) Improved error handling/reporting for standalone BamView application.
+		7) Improved error handling/reporting, although this still needs more work.
 		8) Added buffer sizing to FTPSeekableStream.
 		9) Performance tweak for BAM file indexing.
 		10) Fixed issue in BamView whereby if you went to the end of a long contig and then switched to a shorter one (via the combo), you would end up off the end of the sequence
@@ -34,9 +34,11 @@ Version 17
 	
 	Resized splash screen, as it was too small to the accommodate text info.
 	
+	Updated splash screen logo.
+	
 	Added error handling for dnaplotter template file loading in standalone mode.
 	
-	Added Bioconda recipe. RT ticket #341139 .
+	Bioconda recipe prep work - RT ticket #341139.
 	
 	Fixed RT ticket #467433 - Genbank DBSOURCE field was not recognised by Artemis. DBLINK was already added.
 	

etc/versions

-Artemis Release 17.0.0
-ACT Release 17.0.0
-DNAPlotter Release 17.0.0
-BamView 17.0.0
+Artemis Release 17.0.1
+ACT Release 17.0.1
+DNAPlotter Release 17.0.1
+BamView 17.0.1

uk/ac/sanger/artemis/components/Splash.java

@@ -239,7 +239,7 @@ abstract public class Splash extends JFrame
     }
     
     pack();
-    setSize(450, 275);
+    setSize(455, 280);
 
     final Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
     setLocation(new Point((screen.width - getSize().width) / 2,

uk/ac/sanger/artemis/components/alignment/BamView.java

@@ -62,6 +62,8 @@ import java.io.InputStreamReader;
 import java.lang.management.ManagementFactory;
 import java.lang.management.MemoryMXBean;
 import java.net.URL;
+import java.nio.BufferOverflowException;
+import java.nio.BufferUnderflowException;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Enumeration;
@@ -626,6 +628,11 @@ public class BamView extends JPanel
     	  return exception;
     }
     
+    public short getBamIndex() 
+    {
+    	  return bamIndex;
+    }
+
     public void run() 
     {
     	  exception = null;
@@ -641,7 +648,6 @@ public class BamView extends JPanel
       catch(Exception e)
       {
     	    exception = e;
-        e.printStackTrace();
       }
       finally
       {
@@ -991,14 +997,22 @@ public class BamView extends JPanel
 	          /*
 	           * Check for errors during the bam/cram read process...
 	           */
-	          String errorText = "Error(s): \n";
+	          String errorText = "Failed to load ";
 	          boolean foundErrors = false;
 	          for (BamReadTask task : tasks) 
 	          {
 	        	    if (task.getException() != null)
 	        	    {
 	        	    	  foundErrors = true;
-	        	    	  errorText = errorText + task.getException().getMessage() + "\n";
+	        	    	  
+	        	    	  if (task.getException() instanceof BufferUnderflowException || task.getException() instanceof BufferOverflowException)
+	        	    	    errorText = errorText + bamList.get(task.getBamIndex()) + ".\nThis may be due to an invalid index file.";
+	        	    	  else
+	        	    	    errorText = errorText + bamList.get(task.getBamIndex()) + ".\nError: " + task.getException().getMessage();
+	        	    	  
+	        	    	  logger4j.error(errorText, task.getException());
+	        	    	  
+	        	    	  break;
 	            }
 	          }