X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationRowFilter.java;h=17298ba37e40509216c15237ee61fe2e7df5b69f;hb=68405aa972a7fc07ff21b35c7b2272d1d4ecb1b7;hp=9e205c42dad3be6a4a5059d71b8cf597cb2b0513;hpb=ead72caff9aef9b7103dbb15907aeae777200832;p=jalview.git
diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index 9e205c4..17298ba 100644
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -1,9 +1,26 @@
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.gui;
-import jalview.api.AnnotationRowFilterI;
import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceGroup;
import jalview.schemes.AnnotationColourGradient;
@@ -14,6 +31,7 @@ import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.util.Vector;
+import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JInternalFrame;
@@ -24,8 +42,7 @@ import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
@SuppressWarnings("serial")
-public abstract class AnnotationRowFilter extends JPanel implements
- AnnotationRowFilterI
+public abstract class AnnotationRowFilter extends JPanel
{
protected AlignViewport av;
@@ -54,6 +71,11 @@ public abstract class AnnotationRowFilter extends JPanel implements
protected JTextField thresholdValue = new JTextField(20);
protected JInternalFrame frame;
+
+ protected JButton ok = new JButton();
+
+ protected JButton cancel = new JButton();
+
/**
* enabled if the user is dragging the slider - try to keep updates to a
* minimun
@@ -109,7 +131,6 @@ public abstract class AnnotationRowFilter extends JPanel implements
});
}
-
public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
{
this.av = av;
@@ -121,7 +142,6 @@ public abstract class AnnotationRowFilter extends JPanel implements
}
- @Override
public Vector getAnnotationItems(boolean isSeqAssociated)
{
Vector list = new Vector();
@@ -156,7 +176,6 @@ public abstract class AnnotationRowFilter extends JPanel implements
}
}
}
- // seqAssociated.setEnabled(enableSeqAss);
this.annmap = new int[list.size()];
System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
return list;
@@ -183,7 +202,6 @@ public abstract class AnnotationRowFilter extends JPanel implements
public void ok_actionPerformed(ActionEvent e)
{
- updateView();
try
{
frame.setClosed(true);
@@ -364,78 +382,6 @@ public abstract class AnnotationRowFilter extends JPanel implements
return false;
}
- protected boolean markColumnsContaining(
- AlignmentAnnotation currentAnnotation, int thresholdComparisonType)
- {
- try
- {
- if (currentAnnotation != null)
- {
- Annotation[] annotations = currentAnnotation.annotations;
- ColumnSelection cs = av.getColumnSelection();
- cs.clear();
- if (thresholdComparisonType == AnnotationColourGradient.NO_THRESHOLD)
- {
- int count = 0;
- do
- {
- if (annotations[count] != null)
- {
- if (currentAnnotation.label.equals("Secondary Structure")
- && annotations[count].secondaryStructure != ' ')
- {
- cs.addElement(count);
- }
- else if (currentAnnotation.label
- .equals("Iron Sulphur Contacts"))
- {
- cs.addElement(count);
- }
- else if (annotations[count].value != 0.0)
- {
- cs.addElement(count);
- }
-
- }
- count++;
- } while (count < annotations.length);
- }
- else
- {
- int count = 0;
- do
- {
- if (annotations[count] != null)
- {
- if (thresholdComparisonType == AnnotationColourGradient.ABOVE_THRESHOLD)
- {
- if (annotations[count].value > currentAnnotation.threshold.value)
- {
- cs.addElement(count);
- }
- }
- else if (thresholdComparisonType == AnnotationColourGradient.BELOW_THRESHOLD)
- {
- if (annotations[count].value < currentAnnotation.threshold.value)
- {
- cs.addElement(count);
- }
- }
-
- }
- count++;
- } while (count < annotations.length);
- }
- }
-
- return true;
- } catch (Exception e)
- {
- e.printStackTrace();
- return false;
- }
- }
-
public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
{
return currentAnnotation;
@@ -447,4 +393,9 @@ public abstract class AnnotationRowFilter extends JPanel implements
this.currentAnnotation = currentAnnotation;
}
+ public abstract void valueChanged(boolean updateAllAnnotation);
+
+ public abstract void updateView();
+
+ public abstract void reset();
}