From 1e58b8b312767fca84147372413044d6c152c3c3 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 27 Apr 2007 09:54:13 +0000
Subject: [PATCH] Alignment properties available

---
 src/jalview/appletgui/AlignFrame.java |  164 +++++++++++++++++++++------------
 1 file changed, 105 insertions(+), 59 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index d98d5fb..12a2938 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -711,6 +711,48 @@ public class AlignFrame
     {
       new FeatureSettings(alignPanel);
     }
+    else if(source== alProperties)
+    {
+        StringBuffer contents = new StringBuffer();
+
+        float avg  = 0;
+        int min=Integer.MAX_VALUE, max=0;
+        for(int i=0; i<viewport.alignment.getHeight(); i++)
+        {
+          int size = viewport.alignment.getSequenceAt(i).getEnd()
+              -viewport.alignment.getSequenceAt(i).getStart();
+          avg += size;
+          if(size>max)
+            max = size;
+          if(size<min)
+            min = size;
+        }
+        avg = avg/(float)viewport.alignment.getHeight();
+
+        contents.append("\nSequences: "+ viewport.alignment.getHeight());
+        contents.append("\nMinimum Sequence Length: "+min);
+        contents.append("\nMaximum Sequence Length: "+max);
+        contents.append("\nAverage Length: "+(int)avg);
+
+        if (((Alignment)viewport.alignment).alignmentProperties != null)
+        {
+          Hashtable props = ((Alignment)viewport.alignment).alignmentProperties;
+          Enumeration en = props.keys();
+          while(en.hasMoreElements())
+          {
+            String key = en.nextElement().toString();
+            contents.append("\n"+key+"\t"+props.get(key));
+          }
+        }
+
+        CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
+        cap.setText(contents.toString());
+        Frame frame = new Frame();
+        frame.add(cap);
+        jalview.bin.JalviewLite.addFrame(frame,
+                                         "Alignment Properties: "+getTitle()
+                                         , 400, 250);
+    }
     else if (source == overviewMenuItem)
     {
       overviewMenuItem_actionPerformed();
@@ -2289,65 +2331,66 @@ public class AlignFrame
   //////////////////////////////////////////////////////////////////////////////////
   //JBuilder Graphics here
 
-  protected MenuBar alignFrameMenuBar = new MenuBar();
-  protected Menu fileMenu = new Menu("File");
-  protected MenuItem loadApplication = new MenuItem("View in Full Application");
-  protected MenuItem loadTree = new MenuItem("Load Associated Tree ...");
-  protected MenuItem loadAnnotations = new MenuItem(
+   MenuBar alignFrameMenuBar = new MenuBar();
+   Menu fileMenu = new Menu("File");
+   MenuItem loadApplication = new MenuItem("View in Full Application");
+   MenuItem loadTree = new MenuItem("Load Associated Tree ...");
+   MenuItem loadAnnotations = new MenuItem(
       "Load Features/Annotations ...");
-  protected MenuItem outputFeatures = new MenuItem("Export Features ...");
-  protected MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
-
-  protected MenuItem closeMenuItem = new MenuItem("Close");
-  protected Menu editMenu = new Menu("Edit");
-  protected Menu viewMenu = new Menu("View");
-  protected Menu colourMenu = new Menu("Colour");
-  protected Menu calculateMenu = new Menu("Calculate");
-  protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
-  protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
-  protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
-  protected MenuItem remove2LeftMenuItem = new MenuItem();
-  protected MenuItem remove2RightMenuItem = new MenuItem();
-  protected MenuItem removeGappedColumnMenuItem = new MenuItem();
-  protected MenuItem removeAllGapsMenuItem = new MenuItem();
-  protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
-  protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
-  protected MenuItem sortPairwiseMenuItem = new MenuItem();
-  protected MenuItem sortIDMenuItem = new MenuItem();
-  protected MenuItem sortGroupMenuItem = new MenuItem();
-  protected MenuItem removeRedundancyMenuItem = new MenuItem();
-  protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
-  protected MenuItem PCAMenuItem = new MenuItem();
-  protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
-  protected MenuItem neighbourTreeMenuItem = new MenuItem();
+   MenuItem outputFeatures = new MenuItem("Export Features ...");
+   MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
+
+   MenuItem closeMenuItem = new MenuItem("Close");
+   Menu editMenu = new Menu("Edit");
+   Menu viewMenu = new Menu("View");
+   Menu colourMenu = new Menu("Colour");
+   Menu calculateMenu = new Menu("Calculate");
+   MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
+   MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
+   MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
+   MenuItem remove2LeftMenuItem = new MenuItem();
+   MenuItem remove2RightMenuItem = new MenuItem();
+   MenuItem removeGappedColumnMenuItem = new MenuItem();
+   MenuItem removeAllGapsMenuItem = new MenuItem();
+   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
+   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
+   MenuItem sortPairwiseMenuItem = new MenuItem();
+   MenuItem sortIDMenuItem = new MenuItem();
+   MenuItem sortGroupMenuItem = new MenuItem();
+   MenuItem removeRedundancyMenuItem = new MenuItem();
+   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
+   MenuItem PCAMenuItem = new MenuItem();
+   MenuItem averageDistanceTreeMenuItem = new MenuItem();
+   MenuItem neighbourTreeMenuItem = new MenuItem();
   BorderLayout borderLayout1 = new BorderLayout();
   public Label statusBar = new Label();
-  protected Menu outputTextboxMenu = new Menu();
-  protected MenuItem clustalColour = new MenuItem();
-  protected MenuItem zappoColour = new MenuItem();
-  protected MenuItem taylorColour = new MenuItem();
-  protected MenuItem hydrophobicityColour = new MenuItem();
-  protected MenuItem helixColour = new MenuItem();
-  protected MenuItem strandColour = new MenuItem();
-  protected MenuItem turnColour = new MenuItem();
-  protected MenuItem buriedColour = new MenuItem();
-  protected MenuItem userDefinedColour = new MenuItem();
-  protected MenuItem PIDColour = new MenuItem();
-  protected MenuItem BLOSUM62Colour = new MenuItem();
+   Menu outputTextboxMenu = new Menu();
+   MenuItem clustalColour = new MenuItem();
+   MenuItem zappoColour = new MenuItem();
+   MenuItem taylorColour = new MenuItem();
+   MenuItem hydrophobicityColour = new MenuItem();
+   MenuItem helixColour = new MenuItem();
+   MenuItem strandColour = new MenuItem();
+   MenuItem turnColour = new MenuItem();
+   MenuItem buriedColour = new MenuItem();
+   MenuItem userDefinedColour = new MenuItem();
+   MenuItem PIDColour = new MenuItem();
+   MenuItem BLOSUM62Colour = new MenuItem();
   MenuItem njTreeBlosumMenuItem = new MenuItem();
   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
-  protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
-  protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
+   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
+   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
+   MenuItem alProperties = new MenuItem("Alignment Properties...");
   MenuItem overviewMenuItem = new MenuItem();
-  protected MenuItem undoMenuItem = new MenuItem();
-  protected MenuItem redoMenuItem = new MenuItem();
-  protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+   MenuItem undoMenuItem = new MenuItem();
+   MenuItem redoMenuItem = new MenuItem();
+   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
   MenuItem noColourmenuItem = new MenuItem();
-  protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
-  protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
+   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
+   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
   MenuItem findMenuItem = new MenuItem();
-  protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
-  protected MenuItem nucleotideColour = new MenuItem();
+   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
+   MenuItem nucleotideColour = new MenuItem();
   MenuItem deleteGroups = new MenuItem();
   MenuItem delete = new MenuItem();
   MenuItem copy = new MenuItem();
@@ -2355,23 +2398,23 @@ public class AlignFrame
   Menu pasteMenu = new Menu();
   MenuItem pasteNew = new MenuItem();
   MenuItem pasteThis = new MenuItem();
-  protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
-  protected MenuItem font = new MenuItem();
-  protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
-  protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
-  protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
+   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
+   MenuItem font = new MenuItem();
+   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
+   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
+   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
   MenuItem modifyPID = new MenuItem();
   MenuItem modifyConservation = new MenuItem();
-  protected CheckboxMenuItem autoCalculate
+   CheckboxMenuItem autoCalculate
       = new CheckboxMenuItem("Autocalculate Consensus", true);
-  protected Menu sortByTreeMenu = new Menu();
+   Menu sortByTreeMenu = new Menu();
   Menu sort = new Menu();
   Menu calculate = new Menu();
   MenuItem inputText = new MenuItem();
   Menu helpMenu = new Menu();
   MenuItem documentation = new MenuItem();
   MenuItem about = new MenuItem();
-  protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
+   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
   Panel embeddedMenu;
   Label embeddedEdit;
   Label embeddedSelect;
@@ -2485,6 +2528,7 @@ public class AlignFrame
     annotationPanelMenuItem.addItemListener(this);
     colourTextMenuItem.setLabel("Colour Text");
     colourTextMenuItem.addItemListener(this);
+    alProperties.addActionListener(this);
     overviewMenuItem.setLabel("Overview Window");
     overviewMenuItem.addActionListener(this);
     undoMenuItem.setEnabled(false);
@@ -2630,6 +2674,8 @@ public class AlignFrame
     viewMenu.add(sequenceFeatures);
     viewMenu.add(featureSettings);
     viewMenu.addSeparator();
+    viewMenu.add(alProperties);
+    viewMenu.addSeparator();
     viewMenu.add(overviewMenuItem);
     colourMenu.add(applyToAllGroups);
     colourMenu.addSeparator();
-- 
1.7.10.2