Check if groups have already been added or not

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

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index b720008..314c357 100755 (executable)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -31,8 +31,6 @@ import jalview.io.JalviewFileChooser;
 import java.awt.BorderLayout;\r
 import java.awt.Font;\r
 import java.awt.Color;\r
-import org.biojava.dasobert.dasregistry.DasSource;\r
-import org.biojava.dasobert.dasregistry.DasCoordinateSystem;\r
 \r
 public class FeatureSettings extends JPanel\r
 {\r
@@ -76,7 +74,6 @@ public class FeatureSettings extends JPanel
     if (af.getViewport().featuresDisplayed == null || fr.renderOrder==null)\r
        fr.findAllFeatures();\r
 \r
-\r
     setTableData();\r
 \r
     frame = new JInternalFrame();\r
@@ -85,7 +82,7 @@ public class FeatureSettings extends JPanel
     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
   }\r
 \r
-  public void setTableData()\r
+  synchronized public void setTableData()\r
   {\r
     alignmentHasFeatures = false;\r
 \r
@@ -127,14 +124,28 @@ public class FeatureSettings extends JPanel
              {\r
                visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();\r
              }\r
-             else\r
-             {\r
-               fr.featureGroups.put(group, new Boolean(visible));\r
+\r
                if (groupPanel == null)\r
                {\r
                  groupPanel = new JPanel();\r
                }\r
 \r
+               boolean alreadyAdded = false;\r
+               for(int g=0; g<groupPanel.getComponentCount(); g++)\r
+               {\r
+                 if(((JCheckBox)groupPanel.getComponent(g))\r
+                    .getText().equals(group))\r
+                 {\r
+                   alreadyAdded = true;\r
+                   break;\r
+                 }\r
+               }\r
+\r
+               if(alreadyAdded)\r
+                 continue;\r
+\r
+               fr.featureGroups.put(group, new Boolean(visible));\r
+\r
                final JCheckBox check = new JCheckBox(group, visible);\r
                check.setFont(new Font("Serif", Font.BOLD, 12));\r
                check.addItemListener(new ItemListener()\r
@@ -152,8 +163,6 @@ public class FeatureSettings extends JPanel
                });\r
                groupPanel.add(check);\r
              }\r
-           }\r
-\r
        }\r
 \r
        if (!allFeatures.contains(tmpfeatures[index].getType()))\r
@@ -558,28 +567,34 @@ public class FeatureSettings extends JPanel
   {\r
     Vector selectedSources = dassourceBrowser.getSelectedSources();\r
 \r
-    int uniprotCount = 0;\r
-    for(int i=0; i<selectedSources.size(); i++)\r
+    SequenceI [] dataset, seqs ;\r
+    int iSize;\r
+\r
+    if(af.getViewport().getSelectionGroup()!=null\r
+      && af.getViewport().getSelectionGroup().getSize(false)>0)\r
     {\r
-     DasSource source = (DasSource)selectedSources.elementAt(i);\r
-     DasCoordinateSystem [] coords = source.getCoordinateSystem();\r
-     for(int c=0; c<coords.length; c++)\r
-     {\r
-       if (coords[c].getName().equalsIgnoreCase("UniProt"))\r
-       {\r
-         uniprotCount++;\r
-         break;\r
-       }\r
-     }\r
+      iSize = af.getViewport().getSelectionGroup().getSize(false);\r
+      dataset = new SequenceI[iSize];\r
+      seqs = af.getViewport().getSelectionGroup().\r
+          getSequencesInOrder(\r
+              af.getViewport().getAlignment());\r
+    }\r
+    else\r
+    {\r
+       iSize = af.getViewport().getAlignment().getHeight();\r
+       seqs = af.getViewport().getAlignment().getSequencesArray();\r
     }\r
 \r
-    System.out.println("User selection is "\r
-                       + (((float)uniprotCount/(float)selectedSources.size())*100)\r
-                       +" % Uniprot");\r
+    dataset = new SequenceI[iSize];\r
+    for (int i = 0; i < iSize; i++)\r
+    {\r
+      dataset[i] = seqs[i].getDatasetSequence();\r
+    }\r
 \r
-   new jalview.io.DasSequenceFeatureFetcher(af.getViewport().getAlignment(),\r
-                                             af,\r
-                                            selectedSources);\r
+    new jalview.io.DasSequenceFeatureFetcher(\r
+        dataset,\r
+        af,\r
+        selectedSources);\r
 \r
     af.getViewport().setShowSequenceFeatures(true);\r
     af.showSeqFeatures.setSelected(true);\r