startup file added

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 59717a9..71b326e 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -73,32 +73,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
            av.setSelectionGroup(null);\r
            repaint();\r
            break;\r
-         case KeyEvent.VK_X:\r
-           if(evt.isControlDown())\r
-           alignFrame.cut_actionPerformed(null);\r
-           break;\r
-         case KeyEvent.VK_C:\r
-         if(evt.isControlDown())\r
-           alignFrame.copy_actionPerformed(null);\r
-           break;\r
-         case KeyEvent.VK_V:\r
-          if(evt.isControlDown())\r
-           alignFrame.paste(true);\r
-           break;\r
-         case KeyEvent.VK_A:\r
-         if(evt.isControlDown())\r
-           alignFrame.selectAllSequenceMenuItem_actionPerformed(null);\r
-           break;\r
+\r
         case KeyEvent.VK_DOWN:\r
           alignFrame.moveSelectedSequences(false);\r
           break;\r
         case KeyEvent.VK_UP:\r
           alignFrame.moveSelectedSequences(true);\r
           break;\r
-        case KeyEvent.VK_F:\r
-         if(evt.isControlDown())\r
-          alignFrame.findMenuItem_actionPerformed(null);\r
-          break;\r
        }\r
      }\r
    });\r
@@ -175,12 +156,17 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
    seqPanel.seqCanvas.highlightSearchResults( results );\r
 \r
    // do we need to scroll the panel?\r
-   if(results!=null && (av.getStartSeq()>results[0]\r
-                        || av.getEndSeq()<results[0]\r
-                        || av.getStartRes()>results[1]\r
-                        || av.getEndRes()<results[2]))\r
-       setScrollValues(results[1], results[0]);\r
-\r
+   if(results!=null)\r
+    {\r
+      SequenceI seq = av.alignment.getSequenceAt(results[0]);\r
+      int start = seq.findIndex( results[1] )-1;\r
+      int end = seq.findIndex( results[2] )-1;\r
+      if( av.getStartRes() > start\r
+          || av.getEndRes() < end\r
+          || (av.getStartSeq() > results[0]\r
+          || av.getEndSeq() < results[0]))\r
+        setScrollValues(start, results[0]);\r
+    }\r
 \r
  }\r
 \r
@@ -385,8 +371,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     }\r
     else\r
     {\r
-      if (overviewPanel != null)\r
-        overviewPanel.updateOverviewImage();\r
       setScrollValues(av.getStartRes(), av.getStartSeq());\r
     }\r
 \r
@@ -585,7 +569,10 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     try\r
     {\r
       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
-          "LAST_DIRECTORY"), new String[]{"eps"}, "Encapsulated Postscript");\r
+          "LAST_DIRECTORY"),\r
+              new String[]{"eps"},\r
+              new String[]{"Encapsulated Postscript"},\r
+              "Encapsulated Postscript");\r
       chooser.setFileView(new jalview.io.JalviewFileView());\r
       chooser.setDialogTitle("Create EPS file from alignment");\r
       chooser.setToolTipText("Save");\r
@@ -594,7 +581,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
         return;\r
 \r
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());\r
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());\r
       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
       EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, height);\r
 \r
@@ -634,7 +621,10 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     try\r
     {\r
       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
-          "LAST_DIRECTORY"), new String[]{"png"}, "Portable network graphics");\r
+          "LAST_DIRECTORY"),\r
+              new String[]{"png"},\r
+              new String[]{"Portable network graphics"},\r
+              "Portable network graphics");\r
       chooser.setFileView(new jalview.io.JalviewFileView());\r
       chooser.setDialogTitle("Create EPS file from alignment");\r
       chooser.setToolTipText("Save");\r
@@ -643,7 +633,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
         return;\r
 \r
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());\r
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());\r
       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
 \r
       BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);\r