Better treatment of error states and cancellability in wsclient.

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b217e9c..4fbdb72 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -38,31 +38,20 @@ public class AlignFrame extends GAlignFrame
     try{\r
       String ip = java.net.InetAddress.getLocalHost().getHostAddress();\r
       if( !ip.startsWith("10."))\r
-        alignMenu.setVisible(false);\r
+        webService.setVisible(false);\r
     }\r
     catch(java.net.UnknownHostException e){}\r
-    viewport = new AlignViewport(al,true,true,false);\r
-\r
-    String fontName = jalview.bin.Cache.getProperty("FONT_NAME");\r
-    String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");\r
-    String fontSize = jalview.bin.Cache.getProperty("FONT_SIZE");\r
-    if(fontName!=null && fontStyle!=null && fontSize!=null)\r
-      viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );\r
-\r
-    // add conservation graph to alignment\r
-    viewport.updateConservation();\r
-    viewport.updateConsensus();\r
+    viewport = new AlignViewport(al);\r
 \r
 \r
     alignPanel = new AlignmentPanel(this, viewport);\r
-\r
     alignPanel.annotationPanel.adjustPanelHeight();\r
     alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
     alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
+    alignPanel.setAnnotationVisible( viewport.getShowAnnotation() );\r
 \r
     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
 \r
-\r
     addInternalFrameListener(new InternalFrameAdapter()\r
    {\r
      public void internalFrameActivated(InternalFrameEvent evt)\r
@@ -105,7 +94,7 @@ public class AlignFrame extends GAlignFrame
     {\r
       String choice =  chooser.getSelectedFile().getPath();\r
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
-      String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
+      String output = FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences());\r
       try{\r
         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
         out.println(output);\r
@@ -123,7 +112,7 @@ public class AlignFrame extends GAlignFrame
      cap.formatForOutput();\r
      frame.setContentPane(cap);\r
      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
-     cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
+     cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
   }\r
 \r
   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
@@ -184,7 +173,6 @@ public class AlignFrame extends GAlignFrame
 \r
   Stack historyList = new Stack();\r
   Stack redoList = new Stack();\r
-  JMenuBar jMenuBar1 = new JMenuBar();\r
 \r
   void updateEditMenuBar()\r
   {\r
@@ -244,9 +232,13 @@ public class AlignFrame extends GAlignFrame
     redoList.add(0, new Object[] {history[0], seq});\r
 \r
       seq = (SequenceI[]) history[1];\r
+      AlignmentAnnotation [] old = viewport.alignment.getAlignmentAnnotation();\r
       viewport.setAlignment( new Alignment(seq) );\r
       updateEditMenuBar();\r
+      for(int i=0; i<old.length; i++)\r
+        viewport.alignment.addAnnotation(old[i]);\r
       viewport.updateConsensus();\r
+      viewport.updateConservation();\r
       alignPanel.repaint();\r
   }\r
 \r
@@ -448,6 +440,8 @@ public class AlignFrame extends GAlignFrame
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
   {\r
     viewport.setSelectionGroup(null);\r
+    viewport.getColumnSelection().clear();\r
+    viewport.setSelectionGroup(null);\r
     PaintRefresher.Refresh(null);\r
   }\r
 \r
@@ -460,13 +454,6 @@ public class AlignFrame extends GAlignFrame
     PaintRefresher.Refresh(null);\r
   }\r
 \r
-\r
-  public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-    viewport.getColumnSelection().clear();\r
-    repaint();\r
-  }\r
-\r
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
   {\r
     addHistoryItem("delete columns");\r
@@ -549,19 +536,6 @@ public class AlignFrame extends GAlignFrame
     alignPanel.repaint();\r
   }\r
 \r
-  public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-    char thisChar = '-';\r
-    char nextChar = '.';\r
-    if(viewport.getGapCharacter()=='-')\r
-    {\r
-      thisChar = '.';\r
-      nextChar = '-';\r
-    }\r
-    setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
-    viewport.setGapCharacter(thisChar);\r
-    alignPanel.repaint();\r
-  }\r
 \r
   public void findMenuItem_actionPerformed(ActionEvent e)\r
   {\r
@@ -576,13 +550,7 @@ public class AlignFrame extends GAlignFrame
 \r
   public void font_actionPerformed(ActionEvent e)\r
   {\r
-    JInternalFrame frame = new JInternalFrame();\r
-    FontChooser fc = new FontChooser( alignPanel, frame );\r
-    frame.setContentPane(fc);\r
-    Desktop.addInternalFrame(frame, "Change Font", 480,100, false);\r
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
-    if(alignPanel.getOverviewPanel()!=null)\r
-      alignPanel.getOverviewPanel().updateOverviewImage();\r
+    FontChooser fc = new FontChooser( alignPanel );\r
   }\r
 \r
   protected void fullSeqId_actionPerformed(ActionEvent e)\r
@@ -653,7 +621,7 @@ public class AlignFrame extends GAlignFrame
     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
     {\r
-         AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
+         SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);\r
          ((Alignment)viewport.alignment).featuresAdded = true;\r
     }\r
     alignPanel.repaint();\r
@@ -928,10 +896,7 @@ public class AlignFrame extends GAlignFrame
 \r
   public void userDefinedColour_actionPerformed(ActionEvent e)\r
   {\r
-    JInternalFrame frame = new JInternalFrame();\r
-    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
-    frame.setContentPane(chooser);\r
-    Desktop.addInternalFrame(frame,"User defined colours", 450,540, false );\r
+    UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);\r
   }\r
 \r
   public void PIDColour_actionPerformed(ActionEvent e)\r
@@ -1188,6 +1153,39 @@ public class AlignFrame extends GAlignFrame
 \r
     }\r
   }\r
+  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+    // TODO:resolve which menu item was actually selected\r
+    // Now, check we have enough sequences\r
+      if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)\r
+      {\r
+        // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
+        SequenceGroup seqs = viewport.getSelectionGroup();\r
+        int sz;\r
+        SequenceI[] msa = new SequenceI[sz=seqs.getSize()];\r
+        for (int i = 0; i < sz; i++)\r
+        {\r
+          msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
+        }\r
+\r
+        MsaWSClient ct = new jalview.ws.MsaWSClient(msa);\r
+      }\r
+      else\r
+      {\r
+        Vector seqs = viewport.getAlignment().getSequences();\r
+\r
+        if (seqs.size() > 1) {\r
+          SequenceI[] msa = new SequenceI[seqs.size()];\r
+          for (int i = 0; i < seqs.size(); i++)\r
+          {\r
+            msa[i] = (SequenceI) seqs.elementAt(i);\r
+          }\r
+\r
+          MsaWSClient ct = new MsaWSClient(msa);\r
+        }\r
+\r
+      }\r
+    }\r
 \r
     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
     // Pick the tree file\r