IdentifyFile should not be static

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 35ac570..b714aea 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -691,7 +691,7 @@ public class AlignFrame
       if(str.length()<1)\r
         return;\r
 \r
-      String format = IdentifyFile.Identify(str, "Paste");\r
+      String format = new IdentifyFile().Identify(str, "Paste");\r
       SequenceI[] sequences;\r
 \r
      if(Desktop.jalviewClipboard!=null)\r
@@ -803,24 +803,50 @@ public class AlignFrame
       return;\r
     }\r
 \r
-    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
-                                   HistoryItem.HIDE));\r
 \r
     SequenceGroup sg = viewport.getSelectionGroup();\r
-    boolean allSequences = false;\r
-    if (sg.sequences.size() == viewport.alignment.getHeight())\r
+\r
+\r
+\r
+    //Jalview no longer allows deletion of residues.\r
+    //Check here whether any residues are in selection area\r
+    if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)\r
     {\r
-      allSequences = true;\r
+      for (int i = 0; i < sg.sequences.size(); i++)\r
+      {\r
+        SequenceI seq = sg.getSequenceAt(i);\r
+        int j = sg.getStartRes();\r
+        do\r
+        {\r
+          if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))\r
+          {\r
+            JOptionPane.showInternalMessageDialog(\r
+                Desktop.desktop, "Cannot delete residues from alignment!\n"\r
+                + "Try hiding columns instead.",\r
+                "Deletion of residues not permitted",\r
+                JOptionPane.WARNING_MESSAGE);\r
+\r
+            return;\r
+          }\r
+          j++;\r
+        }while(j<=sg.getEndRes());\r
+      }\r
     }\r
 \r
+\r
+    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
+                                   HistoryItem.HIDE));\r
+\r
+\r
     for (int i = 0; i < sg.sequences.size(); i++)\r
     {\r
       SequenceI seq = sg.getSequenceAt(i);\r
       int index = viewport.getAlignment().findIndex(seq);\r
+\r
       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 \r
       // If the cut affects all sequences, remove highlighted columns\r
-      if (allSequences)\r
+      if (sg.sequences.size() == viewport.alignment.getHeight())\r
       {\r
         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
             sg.getEndRes() + 1);\r
@@ -900,7 +926,6 @@ public class AlignFrame
     viewport.setSelectionGroup(null);\r
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
     alignPanel.idPanel.idCanvas.searchResults = null;\r
-    alignPanel.annotationPanel.activeRes = null;\r
     PaintRefresher.Refresh(null, viewport.alignment);\r
   }\r
 \r
@@ -1194,8 +1219,8 @@ public class AlignFrame
     JInternalFrame frame = new JInternalFrame();\r
     Finder finder = new Finder(viewport, alignPanel, frame);\r
     frame.setContentPane(finder);\r
-    Desktop.addInternalFrame(frame, "Find", 340, 110);\r
     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+    Desktop.addInternalFrame(frame, "Find", 340, 110);\r
   }\r
 \r
   /**\r
@@ -1329,7 +1354,7 @@ public class AlignFrame
       new SequenceFeatureFetcher(viewport.\r
                                  alignment,\r
                                  alignPanel);\r
-      viewport.showSequenceFeatures(true);\r
+      viewport.setShowSequenceFeatures(true);\r
       showSeqFeatures.setSelected(true);\r
     }\r
   }\r
@@ -1347,8 +1372,12 @@ public class AlignFrame
    */\r
   public void showSeqFeatures_actionPerformed(ActionEvent evt)\r
   {\r
-    viewport.showSequenceFeatures(showSeqFeatures.isSelected());\r
+    viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());\r
     alignPanel.repaint();\r
+    if (alignPanel.getOverviewPanel() != null)\r
+    {\r
+      alignPanel.getOverviewPanel().updateOverviewImage();\r
+    }\r
   }\r
 \r
   /**\r
@@ -2627,6 +2656,7 @@ public boolean parseGroupsFile(String file)
     }\r
 \r
     viewport.showSequenceFeatures = true;\r
+    showSeqFeatures.setSelected(true);\r
     alignPanel.repaint();\r
     return true;\r
 }\r
@@ -2704,7 +2734,7 @@ public void drop(DropTargetDropEvent evt)
             if (!isGroupsFile)\r
             {\r
               String protocol = "File";\r
-              String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
+              String format = new IdentifyFile().Identify(file, protocol);\r
               SequenceI[] sequences = new FormatAdapter().readFile(file, protocol, format);\r
 \r
               FastaFile ff = new FastaFile();\r