From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Feb 2006 15:51:07 +0000 (+0000)
Subject: Read startgroup and endgroup in features file
X-Git-Tag: Root_VamJalview_2_07b+~115
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9a4258bfc6277f67d677ce0e62f6ffd6bcc3d436;p=jalview.git

Read startgroup and endgroup in features file
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9bcb759..a70adfc 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -205,8 +205,6 @@ public class AlignFrame
   {
     new SequenceFetcher(this);
   }
-
-
   /**
    * DOCUMENT ME!
    *
@@ -1329,24 +1327,32 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void sequenceFeatures_actionPerformed(ActionEvent evt)
+  public void fetchSeqFeatures_actionPerformed(ActionEvent e)
   {
-    viewport.showSequenceFeatures(sequenceFeatures.isSelected());
-
-    if (viewport.showSequenceFeatures && !viewport.alignment.isNucleotide())
+    if (!viewport.alignment.isNucleotide())
     {
       new SequenceFeatureFetcher(viewport.
-         alignment,
-          alignPanel);
+                                 alignment,
+                                 alignPanel);
+      viewport.showSequenceFeatures(true);
+      showSeqFeatures.setSelected(true);
     }
+  }
 
-    featureSettings.setEnabled(true);
 
+  public void featureSettings_actionPerformed(ActionEvent e)
+  {
+    new FeatureSettings(viewport, alignPanel);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void showSeqFeatures_actionPerformed(ActionEvent evt)
+  {
+    viewport.showSequenceFeatures(showSeqFeatures.isSelected());
     alignPanel.repaint();
   }
 
@@ -2425,10 +2431,7 @@ public class AlignFrame
     }
   }*/
 
-  public void featureSettings_actionPerformed(ActionEvent e)
-  {
-    new FeatureSettings(viewport, alignPanel);
-  }
+
 
 
 
@@ -2556,6 +2559,7 @@ public boolean parseGroupsFile(String file)
       StringTokenizer st;
       SequenceFeature sf;
       int lineNo = 0;
+      String featureGroup = null;
       while ( (line = in.readLine()) != null)
       {
         lineNo++;
@@ -2563,8 +2567,23 @@ public boolean parseGroupsFile(String file)
         if (st.countTokens() == 2)
         {
           type = st.nextToken();
-          UserColourScheme ucs = new UserColourScheme(st.nextToken());
-          alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));
+          if (type.equalsIgnoreCase("startgroup"))
+          {
+            featureGroup = st.nextToken();
+          }
+          else if (type.equalsIgnoreCase("endgroup"))
+          {
+            //We should check whether this is the current group,
+            //but at present theres no way of showing more than 1 group
+            st.nextToken();
+            featureGroup = null;
+          }
+          else
+          {
+            UserColourScheme ucs = new UserColourScheme(st.nextToken());
+            alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type,
+                ucs.findColour("A"));
+          }
           continue;
         }
 
@@ -2597,6 +2616,7 @@ public boolean parseGroupsFile(String file)
           }
 
           sf = new SequenceFeature(type, desc, "", start, end);
+          sf.setFeatureGroup(featureGroup);
 
           seq.getDatasetSequence().addSequenceFeature(sf);
         }