apply version 2.7 copyright

[jalview.git] / src / jalview / gui / SequenceFetcher.java

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index b7cccf7..43c9d42 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -119,7 +119,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       if (guiWindow != null)
       {
         guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
-                initingThread.hashCode());
+                Thread.currentThread().hashCode());
       }
       sfetch = sf;
       _initingFetcher = false;
@@ -229,7 +229,7 @@ public class SequenceFetcher extends JPanel implements Runnable
   {
     this.setLayout(borderLayout2);
 
-    database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    database.setFont(JvSwingUtils.getLabelFont());
     dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
@@ -272,7 +272,7 @@ public class SequenceFetcher extends JPanel implements Runnable
         close_actionPerformed(e);
       }
     });
-    textArea.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    textArea.setFont(JvSwingUtils.getLabelFont());
     textArea.setLineWrap(true);
     textArea.addKeyListener(new KeyAdapter()
     {
@@ -444,9 +444,11 @@ public class SequenceFetcher extends JPanel implements Runnable
       resetDialog();
       return;
     }
-    AlignmentI aresult = null;
+    ArrayList<String> aresultq=new ArrayList<String>();
+    ArrayList<AlignmentI> aresult = new ArrayList<AlignmentI>();
     Object source = database.getSelectedItem();
     Enumeration en = new StringTokenizer(textArea.getText(), ";");
+    boolean isAliSource=false;
     try
     {
       guiWindow.setProgressBar(
@@ -454,6 +456,7 @@ public class SequenceFetcher extends JPanel implements Runnable
               Thread.currentThread().hashCode());
       DbSourceProxy proxy = sfetch.getSourceProxy((String) sources
               .get(source));
+      isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
       if (proxy.getAccessionSeparator() == null)
       {
         while (en.hasMoreElements())
@@ -485,14 +488,8 @@ public class SequenceFetcher extends JPanel implements Runnable
             }
             if (indres != null)
             {
-              if (aresult == null)
-              {
-                aresult = indres;
-              }
-              else
-              {
-                aresult.append(indres);
-              }
+              aresultq.add(item);
+              aresult.add(indres);
             }
           } catch (Exception e)
           {
@@ -514,7 +511,8 @@ public class SequenceFetcher extends JPanel implements Runnable
         }
         try
         {
-          aresult = proxy.getSequenceRecords(multiacc.toString());
+          aresultq.add(multiacc.toString());
+          aresult.add(proxy.getSequenceRecords(multiacc.toString()));
         } catch (OutOfMemoryError oome)
         {
           new OOMWarning("fetching " + multiacc + " from "
@@ -547,9 +545,24 @@ public class SequenceFetcher extends JPanel implements Runnable
               + " from " + database.getSelectedItem());
       e.printStackTrace();
     }
-    if (aresult != null)
+    if (aresult != null && aresult.size()>0)
     {
-      parseResult(aresult, null, null);
+      AlignmentI ar=null;
+      if (isAliSource) {
+        // new window for each result
+        while (aresult.size()>0)
+        {
+          parseResult(aresult.remove(0), aresultq.remove(0)+" "+getDefaultRetrievalTitle(), null);
+        }
+      } else {
+        // concatenate all results in one window
+        while (aresult.size()>0)
+        {
+          if (ar==null) { ar = aresult.remove(0);}
+          else { ar.append(aresult.remove(0)); };
+        }
+        parseResult(ar, null, null);
+      } 
     }
     // only remove visual delay after we finished parsing.
     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
@@ -728,6 +741,13 @@ public class SequenceFetcher extends JPanel implements Runnable
     return null;
   }
 
+  /**
+   * 
+   * @return a standard title for any results retrieved using the currently selected source and settings
+   */
+  public String getDefaultRetrievalTitle() {
+    return "Retrieved from " + database.getSelectedItem();
+  }
   AlignmentI parseResult(AlignmentI al, String title,
           String currentFileFormat)
   {
@@ -748,7 +768,7 @@ public class SequenceFetcher extends JPanel implements Runnable
 
         if (title == null)
         {
-          title = "Retrieved from " + database.getSelectedItem();
+          title = getDefaultRetrievalTitle();
         }
         SequenceFeature[] sfs = null;
         for (Enumeration sq = al.getSequences().elements(); sq