X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColumnChooser.java;h=60775d33790abae4e5679705748b0d72a5641995;hb=refs%2Fheads%2Fbug%2FJAL-2576;hp=c07dfb4a45b95e9f6d4a5da9e736689158b62fba;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationColumnChooser.java b/src/jalview/appletgui/AnnotationColumnChooser.java
index c07dfb4..60775d3 100644
--- a/src/jalview/appletgui/AnnotationColumnChooser.java
+++ b/src/jalview/appletgui/AnnotationColumnChooser.java
@@ -1,7 +1,27 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.appletgui;
 
 import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.util.MessageManager;
 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
@@ -29,7 +49,7 @@ import java.awt.event.TextListener;
 import java.util.Iterator;
 import java.util.Vector;
 
-import javax.swing.JPanel;
+//import javax.swing.JPanel;
 
 //import net.miginfocom.swing.MigLayout;
 
@@ -90,7 +110,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
   private int actionOption = ACTION_OPTION_SELECT;
 
-  private ColumnSelection oldColumnSelection;
+  private HiddenColumns oldHiddenColumns;
 
   public AnnotationColumnChooser()
   {
@@ -115,17 +135,22 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     slider.addAdjustmentListener(this);
     slider.addMouseListener(this);
 
-    if (av.getAlignment().getAlignmentAnnotation() == null)
+    AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+    if (anns == null)
     {
       return;
     }
-    setOldColumnSelection(av.getColumnSelection());
+    setOldHiddenColumns(av.getAlignment().getHiddenColumns());
     adjusting = true;
-    Vector list = new Vector();
+    Vector<String> list = new Vector<String>();
     int index = 1;
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    for (int i = 0; i < anns.length; i++)
     {
-      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+      String label = anns[i].label;
+      if (anns[i].sequenceRef != null)
+      {
+        label = label + "_" + anns[i].sequenceRef.getName();
+      }
       if (!list.contains(label))
       {
         list.addElement(label);
@@ -142,20 +167,22 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     }
 
     populateThresholdComboBox(threshold);
-
+    AnnotationColumnChooser lastChooser = av
+            .getAnnotationColumnSelectionState();
     // restore Object state from the previous session if one exists
-    if (av.getAnnotationColumnSelectionState() != null)
+    if (lastChooser != null)
     {
-      currentSearchPanel = av.getAnnotationColumnSelectionState()
+      currentSearchPanel = lastChooser
               .getCurrentSearchPanel();
-      currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
+      currentStructureFilterPanel = lastChooser
               .getCurrentStructureFilterPanel();
-      annotations.select(av.getAnnotationColumnSelectionState()
+      annotations.select(lastChooser
               .getAnnotations().getSelectedIndex());
-      threshold.select(av.getAnnotationColumnSelectionState()
+      threshold.select(lastChooser
               .getThreshold().getSelectedIndex());
-      actionOption = av.getAnnotationColumnSelectionState()
+      actionOption = lastChooser
               .getActionOption();
+      percentThreshold.setState(lastChooser.percentThreshold.getState());
     }
 
     try
@@ -179,6 +206,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     thresholdValue.setEnabled(false);
     thresholdValue.setColumns(7);
+    thresholdValue.setCaretPosition(0);
 
     ok.addActionListener(this);
     cancel.addActionListener(this);
@@ -194,6 +222,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     // thresholdPanel.setFont(JvSwingUtils.getLabelFont());
     // thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 
+    percentThreshold.setLabel("As percentage");
+    percentThreshold.addItemListener(this);
+
     actionPanel.setBackground(Color.white);
     // actionPanel.setFont(JvSwingUtils.getLabelFont());
 
@@ -217,11 +248,12 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     thresholdPanel.add(getThreshold());
     thresholdPanel.add(slider);
     thresholdPanel.add(thresholdValue);
+    thresholdPanel.add(percentThreshold);
 
     actionPanel.add(ok);
     actionPanel.add(cancel);
 
-    JPanel staticPanel = new JPanel();
+    Panel staticPanel = new Panel();
     staticPanel.setLayout(new BorderLayout());
     staticPanel.setBackground(Color.white);
 
@@ -253,40 +285,42 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     this.validate();
   }
 
+  @Override
   @SuppressWarnings("unchecked")
   public void reset()
   {
-    if (this.getOldColumnSelection() != null)
+    if (this.getOldHiddenColumns() != null)
     {
       av.getColumnSelection().clear();
 
       if (av.getAnnotationColumnSelectionState() != null)
       {
-        ColumnSelection oldSelection = av
+        HiddenColumns oldHidden = av
                 .getAnnotationColumnSelectionState()
-                .getOldColumnSelection();
-        if (oldSelection != null && oldSelection.getHiddenColumns() != null
-                && !oldSelection.getHiddenColumns().isEmpty())
+                .getOldHiddenColumns();
+        if (oldHidden != null && oldHidden.getHiddenRegions() != null
+                && !oldHidden.getHiddenRegions().isEmpty())
         {
-          for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
+          for (Iterator<int[]> itr = oldHidden.getHiddenRegions()
                   .iterator(); itr.hasNext();)
           {
             int positions[] = itr.next();
             av.hideColumns(positions[0], positions[1]);
           }
         }
-        av.setColumnSelection(oldSelection);
+        av.getAlignment().setHiddenColumns(oldHidden);
       }
       ap.paintAlignment(true);
     }
 
   }
 
+  @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     if (!adjusting)
     {
-      thresholdValue.setText((slider.getValue() / 1000f) + "");
+      setThresholdValueText();
       valueChanged(!sliderDragging);
     }
   }
@@ -323,6 +357,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     });
   }
 
+  @Override
   public void valueChanged(boolean updateAllAnnotation)
   {
     if (slider.isEnabled())
@@ -371,12 +406,14 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     slider.setEnabled(true);
     thresholdValue.setEnabled(true);
+    percentThreshold.setEnabled(true);
 
     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
     {
       slider.setEnabled(false);
       thresholdValue.setEnabled(false);
       thresholdValue.setText("");
+      percentThreshold.setEnabled(false);
       // build filter params
     }
     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
@@ -397,16 +434,17 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
-      thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
+      setThresholdValueText();
       // slider.setMajorTickSpacing((int) (range / 10f));
       slider.setEnabled(true);
       thresholdValue.setEnabled(true);
+      percentThreshold.setEnabled(true);
       adjusting = false;
 
       // build filter params
       filterParams
               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
-      if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
+      if (getCurrentAnnotation().isQuantitative())
       {
         filterParams
                 .setThresholdValue(getCurrentAnnotation().threshold.value);
@@ -480,16 +518,16 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     ap.paintAlignment(true);
   }
 
-  public ColumnSelection getOldColumnSelection()
+  public HiddenColumns getOldHiddenColumns()
   {
-    return oldColumnSelection;
+    return oldHiddenColumns;
   }
 
-  public void setOldColumnSelection(ColumnSelection currentColumnSelection)
+  public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
   {
-    if (currentColumnSelection != null)
+    if (currentHiddenColumns != null)
     {
-      this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
+      this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
     }
   }
 
@@ -546,13 +584,21 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     {
       threshold_actionPerformed(null);
     }
+    else if (e.getSource() == percentThreshold)
+    {
+      if (!adjusting)
+      {
+        percentageValue_actionPerformed();
+      }
+
+    }
   }
 
   public void selectedAnnotationChanged()
   {
     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
     if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
-            .getSelectedIndex()].graph != AlignmentAnnotation.NO_GRAPH)
+            .getSelectedIndex()].isQuantitative())
     {
       currentView = AnnotationColumnChooser.GRAPH_VIEW;
     }
@@ -846,21 +892,11 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     }
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
-    if (evt.getSource() == thresholdValue)
-    {
-      try
-      {
-        float f = new Float(thresholdValue.getText()).floatValue();
-        slider.setValue((int) (f * 1000));
-        adjustmentValueChanged(null);
-      } catch (NumberFormatException ex)
-      {
-      }
-    }
 
-    else if (evt.getSource() == ok)
+    if (evt.getSource() == ok)
     {
       ok_actionPerformed(null);
     }