X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=e11f1b484f1aea73fa822b58b35a3a61b64063df;hb=dfa04e77181fccfa6229ffef1591fc9c622d9b39;hp=c2c24622490dc835e25e7df1834f7c86459a973d;hpb=262352d44a49e6102a9e80b0c006ea9331ed0c67;p=jalview.git
diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
old mode 100755
new mode 100644
index c2c2462..e11f1b4
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,20 +1,20 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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.appletgui;
@@ -24,10 +24,10 @@ import java.awt.*;
import java.awt.event.*;
-import jalview.appletgui.FeatureSettings.MyCheckbox;
import jalview.datamodel.*;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
@@ -35,7 +35,7 @@ import jalview.schemes.GraduatedColor;
* @author $author$
* @version $Revision$
*/
-public class FeatureRenderer
+public class FeatureRenderer implements jalview.api.FeatureRenderer
{
AlignViewport av;
@@ -79,12 +79,41 @@ public class FeatureRenderer
}
}
- public void transferSettings(FeatureRenderer fr)
+ public void transferSettings(jalview.api.FeatureRenderer _fr)
{
- renderOrder = fr.renderOrder;
- featureGroups = fr.featureGroups;
- featureColours = fr.featureColours;
- transparency = fr.transparency;
+ if (_fr instanceof FeatureRenderer)
+ {
+ FeatureRenderer fr = (FeatureRenderer) _fr;
+ renderOrder = fr.renderOrder;
+ featureGroups = fr.featureGroups;
+ featureColours = fr.featureColours;
+ transparency = fr.transparency;
+ if (av != null && fr.av != null && fr.av != av)
+ {
+ if (fr.av.featuresDisplayed != null)
+ {
+ if (av.featuresDisplayed == null)
+ {
+ av.featuresDisplayed = new Hashtable();
+ }
+ else
+ {
+ av.featuresDisplayed.clear();
+ }
+ Enumeration en = fr.av.featuresDisplayed.keys();
+ while (en.hasMoreElements())
+ {
+ av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
+ }
+ }
+ }
+ }
+ else
+ {
+ throw new Error(
+ "Implementation error: cannot port feature settings from implementation of type "
+ + _fr.getClass() + " to " + getClass());
+ }
}
static String lastFeatureAdded;
@@ -98,29 +127,33 @@ public class FeatureRenderer
boolean deleteFeature = false;
FeatureColourPanel colourPanel;
- class FeatureColourPanel extends Panel {
- String label="";
-
+
+ class FeatureColourPanel extends Panel
+ {
+ String label = "";
+
private Color maxCol;
- private boolean isColourByLabel,isGcol;
+
+ private boolean isColourByLabel, isGcol;
+
/**
* render a feature style in the amend feature dialog box
*/
public void updateColor(Object newcol)
{
-
- Color bg,col=null;
- GraduatedColor gcol=null;
+
+ Color bg, col = null;
+ GraduatedColor gcol = null;
String vlabel = "";
if (newcol instanceof Color)
{
- isGcol=false;
+ isGcol = false;
col = (Color) newcol;
gcol = null;
}
else if (newcol instanceof GraduatedColor)
{
- isGcol=true;
+ isGcol = true;
gcol = (GraduatedColor) newcol;
col = null;
}
@@ -130,49 +163,57 @@ public class FeatureRenderer
}
if (col != null)
{
- setBackground(bg=col);
+ setBackground(bg = col);
}
else
{
- if (gcol.getThreshType()!=AnnotationColourGradient.NO_THRESHOLD)
+ if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
{
- vlabel += " "+((gcol.getThreshType()==AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)" : "(<)");
+ vlabel += " "
+ + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
+ : "(<)");
}
- if (isColourByLabel=gcol.isColourByLabel()) {
- setBackground(bg=Color.white);
+ if (isColourByLabel = gcol.isColourByLabel())
+ {
+ setBackground(bg = Color.white);
vlabel += " (by Label)";
- } else {
- setBackground(bg=gcol.getMinColor());
+ }
+ else
+ {
+ setBackground(bg = gcol.getMinColor());
maxCol = gcol.getMaxColor();
}
}
- label=vlabel;
+ label = vlabel;
setBackground(bg);
repaint();
}
- FeatureColourPanel() {
+
+ FeatureColourPanel()
+ {
super(null);
}
- public void paint(Graphics g)
+
+ public void paint(Graphics g)
{
- int width=getWidth(),height=getHeight();
- if (isGcol) {
- if (isColourByLabel)
+ Dimension d = getSize();
+ if (isGcol)
{
- g.setColor(Color.white);
- g.fillRect(width/2, 0,width/2, height);
- g.setColor(Color.black);
- Font f=new Font("Verdana", Font.PLAIN,
- 10);
- g.setFont(f);
- g.drawString("Label", 0, 0);
- }
- else
- {
- g.setColor(maxCol);
- g.fillRect(width/2, 0,width/2, height);
-
- }
+ if (isColourByLabel)
+ {
+ g.setColor(Color.white);
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+ g.setColor(Color.black);
+ Font f = new Font("Verdana", Font.PLAIN, 10);
+ g.setFont(f);
+ g.drawString(MessageManager.getString("label.label"), 0, 0);
+ }
+ else
+ {
+ g.setColor(maxCol);
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+
+ }
}
}
@@ -197,7 +238,7 @@ public class FeatureRenderer
final FeatureRenderer fr = this;
Panel panel = new Panel(new GridLayout(3, 1));
-
+
featureIndex = 0; // feature to be amended.
Panel tmp;
@@ -243,7 +284,7 @@ public class FeatureRenderer
ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
}
- Color col = getColour(name.getText());
+ Object col = getFeatureStyle(name.getText());
if (col == null)
{
col = new jalview.schemes.UserColourScheme()
@@ -335,7 +376,7 @@ public class FeatureRenderer
}
else
{
- dialog.ok.setLabel("Amend");
+ dialog.ok.setLabel(MessageManager.getString("label.amend"));
dialog.buttonPanel.add(deleteButton, 1);
deleteButton.addActionListener(new ActionListener()
{
@@ -363,29 +404,22 @@ public class FeatureRenderer
colourPanel.updateColor(fcol);
dialog.setResizable(true);
// TODO: render the graduated color in the box.
- if (fcol instanceof Color)
+ colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
{
- colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
+ public void mousePressed(java.awt.event.MouseEvent evt)
{
- public void mousePressed(java.awt.event.MouseEvent evt)
+ if (!colourPanel.isGcol)
{
new UserDefinedColours(fr, ap.alignFrame);
}
- });
-
- }
- else
- {
- colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
- {
- public void mousePressed(java.awt.event.MouseEvent evt)
+ else
{
- FeatureColourChooser fcc = new FeatureColourChooser(ap.alignFrame, name.getText());
- fcc.setFocusable(true);
+ FeatureColourChooser fcc = new FeatureColourChooser(
+ ap.alignFrame, name.getText());
dialog.transferFocus();
}
- });
- }
+ }
+ });
dialog.setVisible(true);
jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
@@ -412,7 +446,8 @@ public class FeatureRenderer
sf.type = lastFeatureAdded;
sf.featureGroup = lastFeatureGroupAdded;
sf.description = lastDescriptionAdded;
- if (fcol instanceof Color) {
+ if (!colourPanel.isGcol)
+ {
// update colour - otherwise its already done.
setColour(sf.type, colourPanel.getBackground());
}
@@ -456,13 +491,14 @@ public class FeatureRenderer
}
col = colourPanel.getBackground();
- //setColour(lastFeatureAdded, fcol);
+ // setColour(lastFeatureAdded, fcol);
if (lastFeatureGroupAdded != null)
{
featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
}
- if (fcol instanceof Color) {
+ if (fcol instanceof Color)
+ {
setColour(lastFeatureAdded, fcol);
}
av.featuresDisplayed.put(lastFeatureAdded,
@@ -474,17 +510,18 @@ public class FeatureRenderer
tro[0] = renderOrder[renderOrder.length - 1];
System.arraycopy(renderOrder, 0, tro, 1, renderOrder.length - 1);
renderOrder = tro;
-
- ap.paintAlignment(true);
-
- return true;
}
else
{
+ // no update to the alignment
return false;
}
}
-
+ // refresh the alignment and the feature settings dialog
+ if (av.featureSettings != null)
+ {
+ av.featureSettings.refreshTable();
+ }
// findAllFeatures();
ap.paintAlignment(true);
@@ -654,16 +691,16 @@ public class FeatureRenderer
else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
{
- renderFeature(g, seq, seq
- .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
- .findIndex(sequenceFeatures[sfindex].begin) - 1,
+ renderFeature(g, seq,
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
getColour(sequenceFeatures[sfindex])
// new Color(((Integer) av.featuresDisplayed
// .get(sequenceFeatures[sfindex].type)).intValue())
, start, end, y1);
- renderFeature(g, seq, seq
- .findIndex(sequenceFeatures[sfindex].end) - 1, seq
- .findIndex(sequenceFeatures[sfindex].end) - 1,
+ renderFeature(g, seq,
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,
getColour(sequenceFeatures[sfindex])
// new Color(((Integer) av.featuresDisplayed
// .get(sequenceFeatures[sfindex].type)).intValue())
@@ -673,10 +710,11 @@ public class FeatureRenderer
else
{
if (showFeature(sequenceFeatures[sfindex]))
- { renderFeature(g, seq, seq
- .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
- .findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex]), start, end, y1);
+ {
+ renderFeature(g, seq,
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+ getColour(sequenceFeatures[sfindex]), start, end, y1);
}
}
@@ -740,6 +778,20 @@ public class FeatureRenderer
Hashtable minmax = null;
+ /**
+ * Called when alignment in associated view has new/modified features to
+ * discover and display.
+ *
+ */
+ public void featuresAdded()
+ {
+ lastSeq = null;
+ findAllFeatures();
+ }
+
+ /**
+ * find all features on the alignment
+ */
void findAllFeatures()
{
jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
@@ -747,10 +799,10 @@ public class FeatureRenderer
av.featuresDisplayed = new Hashtable();
Vector allfeatures = new Vector();
minmax = new Hashtable();
-
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- SequenceFeature[] features = av.alignment.getSequenceAt(i)
+ SequenceFeature[] features = alignment.getSequenceAt(i)
.getSequenceFeatures();
if (features == null)
@@ -770,8 +822,8 @@ public class FeatureRenderer
{
if (getColour(features[index].getType()) == null)
{
- featureColours.put(features[index].getType(), ucs
- .createColourFromName(features[index].getType()));
+ featureColours.put(features[index].getType(),
+ ucs.createColourFromName(features[index].getType()));
}
av.featuresDisplayed.put(features[index].getType(), new Integer(
@@ -860,6 +912,7 @@ public class FeatureRenderer
throw new Error("Implementation Error: Unrecognised render object "
+ fc.getClass() + " for features of type " + featureType);
}
+
/**
*
* @param sequenceFeature
@@ -871,7 +924,11 @@ public class FeatureRenderer
if (fc instanceof GraduatedColor)
{
return ((GraduatedColor) fc).isColored(sequenceFeature);
- } else { return true; }
+ }
+ else
+ {
+ return true;
+ }
}
/**
@@ -934,7 +991,7 @@ public class FeatureRenderer
for (int i = 0; i < data.length; i++)
{
String type = data[i][0].toString();
- setColour(type, data[i][1]);
+ setColour(type, data[i][1]);
if (((Boolean) data[i][2]).booleanValue())
{
av.featuresDisplayed.put(type, new Integer(getColour(type)
@@ -1020,9 +1077,9 @@ public class FeatureRenderer
for (int i = 0; i < toset.length; i++)
{
Object st = featureGroups.get(toset[i]);
+ featureGroups.put(toset[i], new Boolean(visible));
if (st != null)
{
- featureGroups.put(toset[i], new Boolean(visible));
rdrw = rdrw || (visible != ((Boolean) st).booleanValue());
}
}
@@ -1046,6 +1103,8 @@ public class FeatureRenderer
}
}
+ ArrayList hiddenGroups = new ArrayList();
+
/**
* analyse alignment for groups and hash tables (used to be embedded in
* FeatureSettings.setTableData)
@@ -1059,29 +1118,34 @@ public class FeatureRenderer
{
featureGroups = new Hashtable();
}
- Vector allFeatures = new Vector();
- Vector allGroups = new Vector();
+ hiddenGroups = new ArrayList();
+ hiddenGroups.addAll(featureGroups.keySet());
+ ArrayList allFeatures = new ArrayList();
+ ArrayList allGroups = new ArrayList();
SequenceFeature[] tmpfeatures;
String group;
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+ if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
{
continue;
}
alignmentHasFeatures = true;
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
int index = 0;
while (index < tmpfeatures.length)
{
if (tmpfeatures[index].getFeatureGroup() != null)
{
group = tmpfeatures[index].featureGroup;
+ // Remove group from the hiddenGroup list
+ hiddenGroups.remove(group);
if (!allGroups.contains(group))
{
- allGroups.addElement(group);
+ allGroups.add(group);
boolean visible = true;
if (featureGroups.containsKey(group))
@@ -1097,7 +1161,7 @@ public class FeatureRenderer
if (!allFeatures.contains(tmpfeatures[index].getType()))
{
- allFeatures.addElement(tmpfeatures[index].getType());
+ allFeatures.add(tmpfeatures[index].getType());
}
index++;
}
@@ -1126,16 +1190,17 @@ public class FeatureRenderer
Vector allFeatures = new Vector();
SequenceFeature[] tmpfeatures;
String group;
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+ if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
{
continue;
}
alignmentHasFeatures = true;
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
int index = 0;
while (index < tmpfeatures.length)
{