X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=35690a95f2425796561d25b91b32dc9140f5fdd2;hb=e826112670b160df06adb4030835624248ac4a8a;hp=d8a674ff5440344f6802dba38eaa69cde770cdbf;hpb=720fee2c68d546822739e618942c178e77d87ea8;p=jalview.git
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index d8a674f..35690a9 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1,30 +1,28 @@
/*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
- * 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.
*
- * 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
+ * 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 .
*/
package jalview.gui;
import java.io.*;
import java.util.*;
+import java.util.List;
import java.awt.*;
import java.awt.event.*;
-import java.awt.geom.AffineTransform;
-import java.awt.image.BufferedImage;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
@@ -33,11 +31,13 @@ import javax.swing.event.*;
import javax.swing.table.*;
import jalview.analysis.AlignmentSorter;
+import jalview.bin.Cache;
import jalview.commands.OrderCommand;
import jalview.datamodel.*;
import jalview.io.*;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
public class FeatureSettings extends JPanel
{
@@ -134,7 +134,7 @@ public class FeatureSettings extends JPanel
scrollPane.setViewportView(table);
- dassourceBrowser = new DasSourceBrowser();
+ dassourceBrowser = new DasSourceBrowser(this);
dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
if (af.getViewport().featuresDisplayed == null
@@ -163,16 +163,24 @@ public class FeatureSettings extends JPanel
frame = new JInternalFrame();
frame.setContentPane(this);
- Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450);
- frame
- .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
- {
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- fr.removePropertyChangeListener(change);
- };
- });
+ if (new jalview.util.Platform().isAMac())
+ {
+ Desktop.addInternalFrame(frame, "Sequence Feature Settings", 475, 480);
+ }
+ else
+ {
+ Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450);
+ }
+
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ fr.removePropertyChangeListener(change);
+ dassourceBrowser.fs = null;
+ };
+ });
frame.setLayer(JLayeredPane.PALETTE_LAYER);
}
@@ -272,8 +280,9 @@ public class FeatureSettings extends JPanel
// probably the color chooser!
table.setValueAt(colorChooser.getColor(), selectedRow, 1);
table.validate();
- me.updateFeatureRenderer(((FeatureTableModel) table
- .getModel()).getData(), false);
+ me.updateFeatureRenderer(
+ ((FeatureTableModel) table.getModel()).getData(),
+ false);
}
}
}
@@ -304,15 +313,15 @@ public class FeatureSettings extends JPanel
Vector allGroups = new Vector();
SequenceFeature[] tmpfeatures;
String group;
- for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
+ for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
{
- if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence()
+ if (af.getViewport().getAlignment().getSequenceAt(i).getDatasetSequence()
.getSequenceFeatures() == null)
{
continue;
}
- tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+ tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
.getDatasetSequence().getSequenceFeatures();
int index = 0;
@@ -397,8 +406,8 @@ public class FeatureSettings extends JPanel
{
public void itemStateChanged(ItemEvent evt)
{
- fr.featureGroups.put(check.getText(), new Boolean(check
- .isSelected()));
+ fr.featureGroups.put(check.getText(),
+ new Boolean(check.isSelected()));
af.alignPanel.seqPanel.seqCanvas.repaint();
if (af.alignPanel.overviewPanel != null)
{
@@ -433,10 +442,10 @@ public class FeatureSettings extends JPanel
// Find out which features should be visible depending on which groups
// are selected / deselected
// and recompute average width ordering
- for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
+ for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
{
- tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+ tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
.getDatasetSequence().getSequenceFeatures();
if (tmpfeatures == null)
{
@@ -512,8 +521,8 @@ public class FeatureSettings extends JPanel
data[dataIndex][0] = type;
data[dataIndex][1] = fr.getFeatureStyle(type);
- data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed
- .containsKey(type));
+ data[dataIndex][2] = new Boolean(
+ af.getViewport().featuresDisplayed.containsKey(type));
dataIndex++;
visibleChecks.removeElement(type);
}
@@ -587,10 +596,10 @@ public class FeatureSettings extends JPanel
void load()
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"), new String[]
- { "fc" }, new String[]
- { "Sequence Feature Colours" }, "Sequence Feature Colours");
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+ { "fc" }, new String[]
+ { "Sequence Feature Colours" }, "Sequence Feature Colours");
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle("Load Feature Colours");
chooser.setToolTipText("Load");
@@ -606,15 +615,65 @@ public class FeatureSettings extends JPanel
InputStreamReader in = new InputStreamReader(new FileInputStream(
file), "UTF-8");
- jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
- jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
+ jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
+ jucs = (jalview.schemabinding.version2.JalviewUserColours) jucs
+ .unmarshal(in);
for (int i = jucs.getColourCount() - 1; i >= 0; i--)
{
String name;
- // TODO: update Colour XML
- fr.setColour(name = jucs.getColour(i).getName(), new Color(
- Integer.parseInt(jucs.getColour(i).getRGB(), 16)));
+ jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
+ if (newcol.hasMax())
+ {
+ Color mincol = null, maxcol = null;
+ try
+ {
+ mincol = new Color(Integer.parseInt(newcol.getMinRGB(), 16));
+ maxcol = new Color(Integer.parseInt(newcol.getRGB(), 16));
+
+ } catch (Exception e)
+ {
+ Cache.log.warn("Couldn't parse out graduated feature color.",
+ e);
+ }
+ GraduatedColor gcol = new GraduatedColor(mincol, maxcol,
+ newcol.getMin(), newcol.getMax());
+ if (newcol.hasAutoScale())
+ {
+ gcol.setAutoScaled(newcol.getAutoScale());
+ }
+ if (newcol.hasColourByLabel())
+ {
+ gcol.setColourByLabel(newcol.getColourByLabel());
+ }
+ if (newcol.hasThreshold())
+ {
+ gcol.setThresh(newcol.getThreshold());
+ gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD); // default
+ }
+ if (newcol.getThreshType().length() > 0)
+ {
+ String ttyp = newcol.getThreshType();
+ if (ttyp.equalsIgnoreCase("NONE"))
+ {
+ gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD);
+ }
+ if (ttyp.equalsIgnoreCase("ABOVE"))
+ {
+ gcol.setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
+ }
+ if (ttyp.equalsIgnoreCase("BELOW"))
+ {
+ gcol.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
+ }
+ }
+ fr.setColour(name = newcol.getName(), gcol);
+ }
+ else
+ {
+ fr.setColour(name = jucs.getColour(i).getName(), new Color(
+ Integer.parseInt(jucs.getColour(i).getRGB(), 16)));
+ }
fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount());
}
if (table != null)
@@ -635,10 +694,10 @@ public class FeatureSettings extends JPanel
void save()
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"), new String[]
- { "fc" }, new String[]
- { "Sequence Feature Colours" }, "Sequence Feature Colours");
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+ { "fc" }, new String[]
+ { "Sequence Feature Colours" }, "Sequence Feature Colours");
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle("Save Feature Colour Scheme");
chooser.setToolTipText("Save");
@@ -648,7 +707,7 @@ public class FeatureSettings extends JPanel
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
+ jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
ucs.setSchemeName("Sequence Features");
try
{
@@ -667,12 +726,38 @@ public class FeatureSettings extends JPanel
}
jalview.util.QuickSort.sort(sortOrder, sortTypes);
sortOrder = null;
+ Object fcol;
+ GraduatedColor gcol;
for (i = 0; i < sortTypes.length; i++)
{
- jalview.binding.Colour col = new jalview.binding.Colour();
+ jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
col.setName(sortTypes[i]);
col.setRGB(jalview.util.Format.getHexString(fr.getColour(col
.getName())));
+ fcol = fr.getFeatureStyle(sortTypes[i]);
+ if (fcol instanceof GraduatedColor)
+ {
+ gcol = (GraduatedColor) fcol;
+ col.setMin(gcol.getMin());
+ col.setMax(gcol.getMax());
+ col.setMinRGB(jalview.util.Format.getHexString(gcol
+ .getMinColor()));
+ col.setAutoScale(gcol.isAutoScale());
+ col.setThreshold(gcol.getThresh());
+ col.setColourByLabel(gcol.isColourByLabel());
+ switch (gcol.getThreshType())
+ {
+ case AnnotationColourGradient.NO_THRESHOLD:
+ col.setThreshType("NONE");
+ break;
+ case AnnotationColourGradient.ABOVE_THRESHOLD:
+ col.setThreshType("ABOVE");
+ break;
+ case AnnotationColourGradient.BELOW_THRESHOLD:
+ col.setThreshType("BELOW");
+ break;
+ }
+ }
ucs.addColour(col);
}
ucs.marshal(out);
@@ -819,7 +904,7 @@ public class FeatureSettings extends JPanel
settingsPane.setLayout(borderLayout2);
dasSettingsPane.setLayout(borderLayout3);
bigPanel.setLayout(borderLayout4);
- invert.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ invert.setFont(JvSwingUtils.getLabelFont());
invert.setText("Invert Selection");
invert.addActionListener(new ActionListener()
{
@@ -828,7 +913,7 @@ public class FeatureSettings extends JPanel
invertSelection();
}
});
- optimizeOrder.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ optimizeOrder.setFont(JvSwingUtils.getLabelFont());
optimizeOrder.setText("Optimise Order");
optimizeOrder.addActionListener(new ActionListener()
{
@@ -837,7 +922,7 @@ public class FeatureSettings extends JPanel
orderByAvWidth();
}
});
- sortByScore.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ sortByScore.setFont(JvSwingUtils.getLabelFont());
sortByScore.setText("Seq sort by Score");
sortByScore.addActionListener(new ActionListener()
{
@@ -846,7 +931,7 @@ public class FeatureSettings extends JPanel
sortByScore(null);
}
});
- sortByDens.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ sortByDens.setFont(JvSwingUtils.getLabelFont());
sortByDens.setText("Seq Sort by density");
sortByDens.addActionListener(new ActionListener()
{
@@ -855,7 +940,7 @@ public class FeatureSettings extends JPanel
sortByDens(null);
}
});
- cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ cancel.setFont(JvSwingUtils.getLabelFont());
cancel.setText("Cancel");
cancel.addActionListener(new ActionListener()
{
@@ -865,7 +950,7 @@ public class FeatureSettings extends JPanel
close();
}
});
- ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ ok.setFont(JvSwingUtils.getLabelFont());
ok.setText("OK");
ok.addActionListener(new ActionListener()
{
@@ -874,7 +959,7 @@ public class FeatureSettings extends JPanel
close();
}
});
- loadColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ loadColours.setFont(JvSwingUtils.getLabelFont());
loadColours.setText("Load Colours");
loadColours.addActionListener(new ActionListener()
{
@@ -883,7 +968,7 @@ public class FeatureSettings extends JPanel
load();
}
});
- saveColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ saveColours.setFont(JvSwingUtils.getLabelFont());
saveColours.setText("Save Colours");
saveColours.addActionListener(new ActionListener()
{
@@ -967,18 +1052,30 @@ public class FeatureSettings extends JPanel
gps = getDisplayedFeatureGroups();
if (typ != null)
{
+ ArrayList types = new ArrayList();
for (int i = 0; i < typ.length; i++)
{
- System.err.println("Sorting on Types:" + typ[i]);
+ if (typ[i] != null)
+ {
+ types.add(typ[i]);
+ }
+ typ = new String[types.size()];
+ types.toArray(typ);
}
}
if (gps != null)
{
+ ArrayList grps = new ArrayList();
for (int i = 0; i < gps.length; i++)
{
- System.err.println("Sorting on groups:" + gps[i]);
+ if (gps[i] != null)
+ {
+ grps.add(gps[i]);
+ }
}
+ gps = new String[grps.size()];
+ grps.toArray(gps);
}
AlignmentPanel alignPanel = af.alignPanel;
AlignmentI al = alignPanel.av.getAlignment();
@@ -1068,6 +1165,7 @@ public class FeatureSettings extends JPanel
{
fetchDAS.setEnabled(false);
cancelDAS.setEnabled(true);
+ dassourceBrowser.setGuiEnabled(false);
Vector selectedSources = dassourceBrowser.getSelectedSources();
doDasFeatureFetch(selectedSources, true, true);
}
@@ -1079,7 +1177,7 @@ public class FeatureSettings extends JPanel
* @param checkDbRefs
* @param promptFetchDbRefs
*/
- private void doDasFeatureFetch(Vector selectedSources,
+ private void doDasFeatureFetch(List selectedSources,
boolean checkDbRefs, boolean promptFetchDbRefs)
{
SequenceI[] dataset, seqs;
@@ -1127,9 +1225,9 @@ public class FeatureSettings extends JPanel
* Vector of Strings to resolve to DAS source nicknames.
* @return sources that are present in source list.
*/
- public Vector resolveSourceNicknames(Vector sources)
+ public List resolveSourceNicknames(Vector sources)
{
- return dassourceBrowser.resolveSourceNicknames(sources);
+ return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
}
/**
@@ -1155,14 +1253,14 @@ public class FeatureSettings extends JPanel
public void fetchDasFeatures(Vector sources, boolean block)
{
initDasSources();
- Vector resolved = resolveSourceNicknames(sources);
+ List resolved = dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
if (resolved.size() == 0)
{
resolved = dassourceBrowser.getSelectedSources();
}
if (resolved.size() > 0)
{
- final Vector dassources = resolved;
+ final List dassources = resolved;
fetchDAS.setEnabled(false);
// cancelDAS.setEnabled(true); doDasFetch does this.
Runnable fetcher = new Runnable()
@@ -1195,6 +1293,8 @@ public class FeatureSettings extends JPanel
{
fetchDAS.setEnabled(true);
cancelDAS.setEnabled(false);
+ dassourceBrowser.setGuiEnabled(true);
+
}
public void cancelDAS_actionPerformed(ActionEvent e)
@@ -1203,8 +1303,7 @@ public class FeatureSettings extends JPanel
{
dasFeatureFetcher.cancel();
}
- fetchDAS.setEnabled(true);
- cancelDAS.setEnabled(false);
+ complete();
}
public void noDasSourceActive()
@@ -1297,6 +1396,8 @@ public class FeatureSettings extends JPanel
public ColorRenderer()
{
setOpaque(true); // MUST do this for background to show up.
+ setHorizontalTextPosition(SwingConstants.CENTER);
+ setVerticalTextPosition(SwingConstants.CENTER);
}
public Component getTableCellRendererComponent(JTable table,
@@ -1378,22 +1479,28 @@ public class FeatureSettings extends JPanel
public static void renderGraduatedColor(JLabel comp, GraduatedColor gcol,
int w, int h)
{
-
+ boolean thr = false;
String tt = "";
String tx = "";
if (gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD)
{
- tx += "> ";
+ thr = true;
+ tx += ">";
tt += "Thresholded (Above " + gcol.getThresh() + ") ";
}
if (gcol.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)
{
- tx += "< ";
+ thr = true;
+ tx += "<";
tt += "Thresholded (Below " + gcol.getThresh() + ") ";
}
if (gcol.isColourByLabel())
{
tt = "Coloured by label text. " + tt;
+ if (thr)
+ {
+ tx += " ";
+ }
tx += "Label";
comp.setIcon(null);
}
@@ -1401,14 +1508,15 @@ public class FeatureSettings extends JPanel
{
Color newColor = gcol.getMaxColor();
comp.setBackground(newColor);
- System.err.println("Width is " + w / 2);
- Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w / 2, h);
+ // System.err.println("Width is " + w / 2);
+ Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
comp.setIcon(ficon);
// tt+="RGB value: Max (" + newColor.getRed() + ", "
// + newColor.getGreen() + ", " + newColor.getBlue()
// + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
// + ", " + minCol.getBlue() + ")");
}
+ comp.setHorizontalAlignment(SwingConstants.CENTER);
comp.setText(tx);
if (tt.length() > 0)
{
@@ -1430,14 +1538,31 @@ class FeatureIcon implements Icon
Color backg;
+ boolean midspace = false;
+
int width = 50, height = 20;
- FeatureIcon(GraduatedColor gfc, Color bg, int w, int h)
+ int s1, e1; // start and end of midpoint band for thresholded symbol
+
+ Color mpcolour = Color.white;
+
+ FeatureIcon(GraduatedColor gfc, Color bg, int w, int h, boolean mspace)
{
gcol = gfc;
backg = bg;
width = w;
height = h;
+ midspace = mspace;
+ if (midspace)
+ {
+ s1 = width / 3;
+ e1 = s1 * 2;
+ }
+ else
+ {
+ s1 = width / 2;
+ e1 = s1;
+ }
}
public int getIconWidth()
@@ -1474,7 +1599,14 @@ class FeatureIcon implements Icon
{
Color minCol = gcol.getMinColor();
g.setColor(minCol);
- g.fillRect(0, 0, width, height);
+ g.fillRect(0, 0, s1, height);
+ if (midspace)
+ {
+ g.setColor(Color.white);
+ g.fillRect(s1, 0, e1 - s1, height);
+ }
+ g.setColor(gcol.getMaxColor());
+ g.fillRect(0, e1, width - e1, height);
}
}
}