/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
- *
- * 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 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
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import java.util.*;
+import java.util.concurrent.ConcurrentHashMap;
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
import jalview.datamodel.*;
+import jalview.schemes.GraduatedColor;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class FeatureRenderer
+public class FeatureRenderer implements jalview.api.FeatureRenderer
{
+ AlignmentPanel ap;
+
AlignViewport av;
+
Color resBoxColour;
+
+ /**
+ * global transparency for feature
+ */
float transparency = 1.0f;
+
FontMetrics fm;
+
int charOffset;
- Hashtable featureColours = new Hashtable();
+ Map featureColours = new ConcurrentHashMap();
// A higher level for grouping features of a
// particular type
- Hashtable featureGroups = null;
+ Map featureGroups = new ConcurrentHashMap();
// This is actually an Integer held in the hashtable,
// Retrieved using the key feature type
Object currentColour;
String[] renderOrder;
- PropertyChangeSupport changeSupport=new PropertyChangeSupport(this);
+
+ PropertyChangeSupport changeSupport = new PropertyChangeSupport(this);
Vector allfeatures;
/**
* Creates a new FeatureRenderer object.
- *
+ *
* @param av
* DOCUMENT ME!
*/
- public FeatureRenderer(AlignViewport av)
+ public FeatureRenderer(AlignmentPanel ap)
{
- this.av = av;
+ this.ap = ap;
+ this.av = ap.av;
+ if (ap != null && ap.seqPanel != null && ap.seqPanel.seqCanvas != null
+ && ap.seqPanel.seqCanvas.fr != null)
+ {
+ transferSettings(ap.seqPanel.seqCanvas.fr);
+ }
}
+ public class FeatureRendererSettings implements Cloneable
+ {
+ String[] renderOrder;
+
+ Map featureGroups;
+
+ Map featureColours;
+
+ float transparency;
+
+ Map featureOrder;
+
+ public FeatureRendererSettings(String[] renderOrder,
+ Hashtable featureGroups, Hashtable featureColours,
+ float transparency, Hashtable featureOrder)
+ {
+ super();
+ this.renderOrder = renderOrder;
+ this.featureGroups = featureGroups;
+ this.featureColours = featureColours;
+ this.transparency = transparency;
+ this.featureOrder = featureOrder;
+ }
+
+ /**
+ * create an independent instance of the feature renderer settings
+ *
+ * @param fr
+ */
+ public FeatureRendererSettings(FeatureRenderer fr)
+ {
+ renderOrder = null;
+ featureGroups = new ConcurrentHashMap();
+ featureColours = new ConcurrentHashMap();
+ featureOrder = new ConcurrentHashMap();
+ if (fr.renderOrder != null)
+ {
+ this.renderOrder = new String[fr.renderOrder.length];
+ System.arraycopy(fr.renderOrder, 0, renderOrder, 0,
+ fr.renderOrder.length);
+ }
+ if (fr.featureGroups != null)
+ {
+ this.featureGroups = new ConcurrentHashMap(fr.featureGroups);
+ }
+ if (fr.featureColours != null)
+ {
+ this.featureColours = new ConcurrentHashMap(fr.featureColours);
+ }
+ Iterator en = fr.featureColours.keySet().iterator();
+ while (en.hasNext())
+ {
+ Object next = en.next();
+ Object val = featureColours.get(next);
+ if (val instanceof GraduatedColor)
+ {
+ featureColours
+ .put(next, new GraduatedColor((GraduatedColor) val));
+ }
+ }
+ this.transparency = fr.transparency;
+ if (fr.featureOrder != null)
+ {
+ this.featureOrder = new ConcurrentHashMap(fr.featureOrder);
+ }
+ }
+ }
+
+ public FeatureRendererSettings getSettings()
+ {
+ return new FeatureRendererSettings(this);
+ }
+
+ public void transferSettings(FeatureRendererSettings fr)
+ {
+ this.renderOrder = fr.renderOrder;
+ this.featureGroups = fr.featureGroups;
+ this.featureColours = fr.featureColours;
+ this.transparency = fr.transparency;
+ this.featureOrder = fr.featureOrder;
+ }
+
+ /**
+ * update from another feature renderer
+ *
+ * @param fr
+ * settings to copy
+ */
public void transferSettings(FeatureRenderer fr)
{
- renderOrder = fr.renderOrder;
- featureGroups = fr.featureGroups;
- featureColours = fr.featureColours;
- transparency = fr.transparency;
- featureOrder = fr.featureOrder;
+ FeatureRendererSettings frs = new FeatureRendererSettings(fr);
+ this.renderOrder = frs.renderOrder;
+ this.featureGroups = frs.featureGroups;
+ this.featureColours = frs.featureColours;
+ this.transparency = frs.transparency;
+ this.featureOrder = frs.featureOrder;
+ if (av != null && av != fr.av)
+ {
+ // copy over the displayed feature settings
+ if (fr.av != null)
+ {
+ if (fr.av.featuresDisplayed != null)
+ {
+ // update display settings
+ if (av.featuresDisplayed == null)
+ {
+ av.featuresDisplayed = new Hashtable(fr.av.featuresDisplayed);
+ }
+ else
+ {
+ av.featuresDisplayed.clear();
+ Enumeration en = fr.av.featuresDisplayed.keys();
+ while (en.hasMoreElements())
+ {
+ av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
+ }
+
+ }
+ }
+ }
+ }
}
BufferedImage offscreenImage;
+
boolean offscreenRender = false;
+
public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
{
- return new Color(findFeatureColour(initialCol.getRGB(),
- seq, res));
+ return new Color(findFeatureColour(initialCol.getRGB(), seq, res));
}
/**
* This is used by the Molecule Viewer and Overview to get the accurate
* colourof the rendered sequence
*/
- public int findFeatureColour(int initialCol, SequenceI seq, int column)
+ public synchronized int findFeatureColour(int initialCol, SequenceI seq,
+ int column)
{
if (!av.showSequenceFeatures)
{
{
lastSeq = seq;
sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
- if (sequenceFeatures!=null)
+ if (sequenceFeatures != null)
{
sfSize = sequenceFeatures.length;
}
}
- if (sequenceFeatures!=lastSeq.getDatasetSequence().getSequenceFeatures()) {
+ if (sequenceFeatures != lastSeq.getDatasetSequence()
+ .getSequenceFeatures())
+ {
sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
if (sequenceFeatures != null)
{
}
}
- if (sequenceFeatures == null)
+ if (sequenceFeatures == null || sfSize == 0)
{
return initialCol;
}
-
if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
{
return Color.white.getRGB();
}
currentColour = null;
-
+ // TODO: non-threadsafe - each rendering thread needs its own instance of
+ // the feature renderer - or this should be synchronized.
offscreenRender = true;
if (offscreenImage != null)
{
offscreenImage.setRGB(0, 0, initialCol);
- drawSequence(offscreenImage.getGraphics(),
- lastSeq,
- column, column, 0);
+ drawSequence(offscreenImage.getGraphics(), lastSeq, column, column, 0);
return offscreenImage.getRGB(0, 0);
}
else
{
- drawSequence(null,
- lastSeq,
- lastSeq.findPosition(column),
- -1, -1);
+ drawSequence(null, lastSeq, lastSeq.findPosition(column), -1, -1);
if (currentColour == null)
{
}
else
{
- return ( (Integer) currentColour).intValue();
+ return ((Integer) currentColour).intValue();
}
}
/**
* DOCUMENT ME!
- *
+ *
* @param g
* DOCUMENT ME!
* @param seq
// String type;
// SequenceFeature sf;
SequenceI lastSeq;
+
SequenceFeature[] sequenceFeatures;
+
int sfSize, sfindex, spos, epos;
- public void drawSequence(Graphics g, SequenceI seq,
- int start, int end, int y1)
+ /**
+ * show scores as heights
+ */
+ protected boolean varyHeight = false;
+
+ synchronized public void drawSequence(Graphics g, SequenceI seq,
+ int start, int end, int y1)
{
+
if (seq.getDatasetSequence().getSequenceFeatures() == null
- || seq.getDatasetSequence().getSequenceFeatures().length == 0)
+ || seq.getDatasetSequence().getSequenceFeatures().length == 0)
{
return;
}
fm = g.getFontMetrics();
}
- if (av.featuresDisplayed == null
- || renderOrder == null
- || newFeatureAdded)
+ if (av.featuresDisplayed == null || renderOrder == null
+ || newFeatureAdded)
{
findAllFeatures();
if (av.featuresDisplayed.size() < 1)
}
sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
- sfSize = sequenceFeatures.length;
}
- if (lastSeq == null || seq != lastSeq
- || seq.getDatasetSequence().getSequenceFeatures()!=sequenceFeatures)
+ if (lastSeq == null
+ || seq != lastSeq
+ || seq.getDatasetSequence().getSequenceFeatures() != sequenceFeatures)
{
lastSeq = seq;
sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
- sfSize = sequenceFeatures.length;
}
if (transparency != 1 && g != null)
{
Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(
- AlphaComposite.getInstance(
- AlphaComposite.SRC_OVER, transparency));
+ g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
+ transparency));
}
if (!offscreenRender)
epos = lastSeq.findPosition(end);
}
+ sfSize = sequenceFeatures.length;
String type;
for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
{
// current feature to render
for (sfindex = 0; sfindex < sfSize; sfindex++)
{
- if (sequenceFeatures.length <= sfindex)
- {
- continue;
- }
if (!sequenceFeatures[sfindex].type.equals(type))
{
continue;
}
if (featureGroups != null
- && sequenceFeatures[sfindex].featureGroup != null
- &&
- featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
- &&
- ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
- featureGroup)).
- booleanValue())
+ && sequenceFeatures[sfindex].featureGroup != null
+ && sequenceFeatures[sfindex].featureGroup.length() != 0
+ && featureGroups
+ .containsKey(sequenceFeatures[sfindex].featureGroup)
+ && !((Boolean) featureGroups
+ .get(sequenceFeatures[sfindex].featureGroup))
+ .booleanValue())
{
continue;
}
- if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
- || sequenceFeatures[sfindex].getEnd() < spos))
+ if (!offscreenRender
+ && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex]
+ .getEnd() < spos))
{
continue;
}
if (offscreenRender && offscreenImage == null)
{
- if (sequenceFeatures[sfindex].begin <= start &&
- sequenceFeatures[sfindex].end >= start)
+ if (sequenceFeatures[sfindex].begin <= start
+ && sequenceFeatures[sfindex].end >= start)
{
- currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
- type);
+ // this is passed out to the overview and other sequence renderers
+ // (e.g. molecule viewer) to get displayed colour for rendered
+ // sequence
+ currentColour = new Integer(
+ getColour(sequenceFeatures[sfindex]).getRGB());
+ // used to be retreived from av.featuresDisplayed
+ // currentColour = av.featuresDisplayed
+ // .get(sequenceFeatures[sfindex].type);
+
}
}
else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
{
renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- new Color( ( (Integer) av.featuresDisplayed.get(
- sequenceFeatures[sfindex].type)).intValue()),
- start, end, y1);
+ 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,
- new Color( ( (Integer) av.featuresDisplayed.get(
- sequenceFeatures[sfindex].type)).intValue()),
- start, end, y1);
+ 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())
+ , start, end, y1);
}
- else
+ else if (showFeature(sequenceFeatures[sfindex]))
{
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex].type),
- start, end, y1);
+ if (av.showSeqFeaturesHeight
+ && sequenceFeatures[sfindex].score != Float.NaN)
+ {
+ renderScoreFeature(g, seq,
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+ getColour(sequenceFeatures[sfindex]), start, end, y1,
+ normaliseScore(sequenceFeatures[sfindex]));
+ }
+ else
+ {
+ renderFeature(g, seq,
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+ getColour(sequenceFeatures[sfindex]), start, end, y1);
+ }
}
}
if (transparency != 1.0f && g != null)
{
Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(
- AlphaComposite.getInstance(
- AlphaComposite.SRC_OVER, 1.0f));
+ g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
+ 1.0f));
}
}
+ Hashtable minmax = new Hashtable();
+
+ /**
+ * normalise a score against the max/min bounds for the feature type.
+ *
+ * @param sequenceFeature
+ * @return byte[] { signed, normalised signed (-127 to 127) or unsigned
+ * (0-255) value.
+ */
+ private final byte[] normaliseScore(SequenceFeature sequenceFeature)
+ {
+ float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0];
+ final byte[] r = new byte[]
+ { 0, (byte) 255 };
+ if (mm != null)
+ {
+ if (r[0] != 0 || mm[0] < 0.0)
+ {
+ r[0] = 1;
+ r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1]));
+ }
+ else
+ {
+ r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1]));
+ }
+ }
+ return r;
+ }
+
char s;
+
int i;
- void renderFeature(Graphics g, SequenceI seq,
- int fstart, int fend, Color featureColour, int start,
- int end, int y1)
+
+ void renderFeature(Graphics g, SequenceI seq, int fstart, int fend,
+ Color featureColour, int start, int end, int y1)
{
- if ( ( (fstart <= end) && (fend >= start)))
+ if (((fstart <= end) && (fend >= start)))
{
if (fstart < start)
{ // fix for if the feature we have starts before the sequence start,
g.setColor(featureColour);
- g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
+ g.fillRect((i - start) * av.charWidth, y1, av.charWidth,
+ av.charHeight);
if (offscreenRender || !av.validCharWidth)
{
g.setColor(Color.white);
charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s),
- charOffset + (av.charWidth * (i - start)),
- pady);
+ g.drawString(String.valueOf(s), charOffset
+ + (av.charWidth * (i - start)), pady);
+
+ }
+ }
+ }
+
+ void renderScoreFeature(Graphics g, SequenceI seq, int fstart, int fend,
+ Color featureColour, int start, int end, int y1, byte[] bs)
+ {
+
+ if (((fstart <= end) && (fend >= start)))
+ {
+ if (fstart < start)
+ { // fix for if the feature we have starts before the sequence start,
+ fstart = start; // but the feature end is still valid!!
+ }
+
+ if (fend >= end)
+ {
+ fend = end;
+ }
+ int pady = (y1 + av.charHeight) - av.charHeight / 5;
+ int ystrt = 0, yend = av.charHeight;
+ if (bs[0] != 0)
+ {
+ // signed - zero is always middle of residue line.
+ if (bs[1] < 128)
+ {
+ yend = av.charHeight * (128 - bs[1]) / 512;
+ ystrt = av.charHeight - yend / 2;
+ }
+ else
+ {
+ ystrt = av.charHeight / 2;
+ yend = av.charHeight * (bs[1] - 128) / 512;
+ }
+ }
+ else
+ {
+ yend = av.charHeight * bs[1] / 255;
+ ystrt = av.charHeight - yend;
+
+ }
+ for (i = fstart; i <= fend; i++)
+ {
+ s = seq.getCharAt(i);
+
+ if (jalview.util.Comparison.isGap(s))
+ {
+ continue;
+ }
+
+ g.setColor(featureColour);
+ int x = (i - start) * av.charWidth;
+ g.drawRect(x, y1, av.charWidth, av.charHeight);
+ g.fillRect(x, y1 + ystrt, av.charWidth, yend);
+
+ if (offscreenRender || !av.validCharWidth)
+ {
+ continue;
+ }
+
+ g.setColor(Color.black);
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ g.drawString(String.valueOf(s), charOffset
+ + (av.charWidth * (i - start)), pady);
}
}
}
boolean newFeatureAdded = false;
+
/**
- * Called when alignment in associated view has new/modified features
- * to discover and display.
- *
+ * Called when alignment in associated view has new/modified features to
+ * discover and display.
+ *
*/
public void featuresAdded()
{
- lastSeq=null;
+ lastSeq = null;
findAllFeatures();
}
boolean findingFeatures = false;
+
/**
* search the alignment for all new features, give them a colour and display
* them. Then fires a PropertyChangeEvent on the changeSupport object.
- *
+ *
*/
- synchronized void findAllFeatures()
+ void findAllFeatures()
{
- findAllFeatures(true); // add all new features as visible
- if (!firing) {
- firing=true;
- changeSupport.firePropertyChange("changeSupport",null,null);
- firing=false;
+ synchronized (firing)
+ {
+ if (firing.equals(Boolean.FALSE))
+ {
+ firing = Boolean.TRUE;
+ findAllFeatures(true); // add all new features as visible
+ changeSupport.firePropertyChange("changeSupport", null, null);
+ firing = Boolean.FALSE;
+ }
}
}
+
/**
* Searches alignment for all features and updates colours
- *
+ *
* @param newMadeVisible
* if true newly added feature types will be rendered immediatly
*/
- synchronized void findAllFeatures(boolean newMadeVisible) {
+ synchronized void findAllFeatures(boolean newMadeVisible)
+ {
newFeatureAdded = false;
if (findingFeatures)
allfeatures = new Vector();
Vector oldfeatures = new Vector();
- if (renderOrder!=null)
+ if (renderOrder != null)
{
- for (int i=0; i<renderOrder.length; i++) {
- if (renderOrder[i]!=null)
+ for (int i = 0; i < renderOrder.length; i++)
+ {
+ if (renderOrder[i] != null)
{
oldfeatures.addElement(renderOrder[i]);
}
}
}
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ if (minmax == null)
+ {
+ minmax = new Hashtable();
+ }
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- SequenceFeature[] features
- = av.alignment.getSequenceAt(i).getDatasetSequence().
- getSequenceFeatures();
+ SequenceFeature[] features = alignment.getSequenceAt(i)
+ .getDatasetSequence().getSequenceFeatures();
if (features == null)
{
{
if (!av.featuresDisplayed.containsKey(features[index].getType()))
{
- if (! (features[index].begin == 0 && features[index].end == 0))
+
+ if (featureGroups.containsKey(features[index].getType()))
+ {
+ boolean visible = ((Boolean) featureGroups
+ .get(features[index].featureGroup)).booleanValue();
+
+ if (!visible)
+ {
+ index++;
+ continue;
+ }
+ }
+
+ if (!(features[index].begin == 0 && features[index].end == 0))
{
// If beginning and end are 0, the feature is for the whole sequence
// and we don't want to render the feature in the normal way
- if (newMadeVisible && !oldfeatures.contains(features[index].getType())) {
+ if (newMadeVisible
+ && !oldfeatures.contains(features[index].getType()))
+ {
// this is a new feature type on the alignment. Mark it for
// display.
av.featuresDisplayed.put(features[index].getType(),
- new Integer(getColour(features[index].
- getType()).getRGB()));
- setOrder(features[index].getType(),0);
+ new Integer(getColour(features[index].getType())
+ .getRGB()));
+ setOrder(features[index].getType(), 0);
}
- }
+ }
}
if (!allfeatures.contains(features[index].getType()))
{
allfeatures.addElement(features[index].getType());
}
+ if (features[index].score != Float.NaN)
+ {
+ int nonpos = features[index].getBegin() >= 1 ? 0 : 1;
+ float[][] mm = (float[][]) minmax.get(features[index].getType());
+ if (mm == null)
+ {
+ mm = new float[][]
+ { null, null };
+ minmax.put(features[index].getType(), mm);
+ }
+ if (mm[nonpos] == null)
+ {
+ mm[nonpos] = new float[]
+ { features[index].score, features[index].score };
+
+ }
+ else
+ {
+ if (mm[nonpos][0] > features[index].score)
+ {
+ mm[nonpos][0] = features[index].score;
+ }
+ if (mm[nonpos][1] < features[index].score)
+ {
+ mm[nonpos][1] = features[index].score;
+ }
+ }
+ }
index++;
}
}
updateRenderOrder(allfeatures);
findingFeatures = false;
}
- protected boolean firing=false;
+
+ protected Boolean firing = Boolean.FALSE;
+
/**
- * replaces the current renderOrder with the unordered features in allfeatures.
- * The ordering of any types in both renderOrder and allfeatures is preserved,
- * and all new feature types are rendered on top of the existing types, in
- * the order given by getOrder or the order given in allFeatures.
+ * replaces the current renderOrder with the unordered features in
+ * allfeatures. The ordering of any types in both renderOrder and allfeatures
+ * is preserved, and all new feature types are rendered on top of the existing
+ * types, in the order given by getOrder or the order given in allFeatures.
* Note. this operates directly on the featureOrder hash for efficiency. TODO:
* eliminate the float storage for computing/recalling the persistent ordering
- *
+ * New Cability: updates min/max for colourscheme range if its dynamic
+ *
* @param allFeatures
*/
- private void updateRenderOrder(Vector allFeatures) {
+ private void updateRenderOrder(Vector allFeatures)
+ {
Vector allfeatures = new Vector(allFeatures);
String[] oldRender = renderOrder;
renderOrder = new String[allfeatures.size()];
- boolean initOrders=(featureOrder==null);
- int opos=0;
- if (oldRender!=null && oldRender.length>0)
+ Object mmrange, fc = null;
+ boolean initOrders = (featureOrder == null);
+ int opos = 0;
+ if (oldRender != null && oldRender.length > 0)
{
- for (int j=0; j<oldRender.length; j++)
+ for (int j = 0; j < oldRender.length; j++)
{
- if (oldRender[j]!=null)
+ if (oldRender[j] != null)
+ {
+ if (initOrders)
{
- if (initOrders)
+ setOrder(oldRender[j], (1 - (1 + (float) j)
+ / (float) oldRender.length));
+ }
+ if (allfeatures.contains(oldRender[j]))
+ {
+ renderOrder[opos++] = oldRender[j]; // existing features always
+ // appear below new features
+ allfeatures.removeElement(oldRender[j]);
+ if (minmax != null)
{
- setOrder(oldRender[j], (1-(1+(float)j)/(float) oldRender.length));
- }
- if (allfeatures.contains(oldRender[j])) {
- renderOrder[opos++] = oldRender[j]; // existing features always
- // appear below new features
- allfeatures.removeElement(oldRender[j]);
+ mmrange = minmax.get(oldRender[j]);
+ if (mmrange != null)
+ {
+ fc = featureColours.get(oldRender[j]);
+ if (fc != null && fc instanceof GraduatedColor
+ && ((GraduatedColor) fc).isAutoScale())
+ {
+ ((GraduatedColor) fc).updateBounds(
+ ((float[][]) mmrange)[0][0],
+ ((float[][]) mmrange)[0][1]);
+ }
+ }
}
}
}
+ }
}
- if (allfeatures.size()==0) {
+ if (allfeatures.size() == 0)
+ {
// no new features - leave order unchanged.
return;
}
- int i=allfeatures.size()-1;
- int iSize=i;
- boolean sort=false;
+ int i = allfeatures.size() - 1;
+ int iSize = i;
+ boolean sort = false;
String[] newf = new String[allfeatures.size()];
float[] sortOrder = new float[allfeatures.size()];
Enumeration en = allfeatures.elements();
while (en.hasMoreElements())
{
newf[i] = en.nextElement().toString();
+ if (minmax != null)
+ {
+ // update from new features minmax if necessary
+ mmrange = minmax.get(newf[i]);
+ if (mmrange != null)
+ {
+ fc = featureColours.get(newf[i]);
+ if (fc != null && fc instanceof GraduatedColor
+ && ((GraduatedColor) fc).isAutoScale())
+ {
+ ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0],
+ ((float[][]) mmrange)[0][1]);
+ }
+ }
+ }
if (initOrders || !featureOrder.containsKey(newf[i]))
{
int denom = initOrders ? allfeatures.size() : featureOrder.size();
- // new unordered feature - compute persistent ordering at head of
- // existing features.
- setOrder(newf[i], i/(float) denom);
+ // new unordered feature - compute persistent ordering at head of
+ // existing features.
+ setOrder(newf[i], i / (float) denom);
}
// set order from newly found feature from persisted ordering.
- sortOrder[i] = 2-((Float) featureOrder.get(newf[i])).floatValue();
- if (i<iSize)
+ sortOrder[i] = 2 - ((Float) featureOrder.get(newf[i])).floatValue();
+ if (i < iSize)
{
// only sort if we need to
- sort = sort || sortOrder[i]>sortOrder[i+1];
+ sort = sort || sortOrder[i] > sortOrder[i + 1];
}
i--;
}
- if (iSize>1 && sort)
+ if (iSize > 1 && sort)
+ {
jalview.util.QuickSort.sort(sortOrder, newf);
- sortOrder=null;
+ }
+ sortOrder = null;
System.arraycopy(newf, 0, renderOrder, opos, newf.length);
}
- public Color getColour(String featureType)
+
+ /**
+ * get a feature style object for the given type string. Creates a
+ * java.awt.Color for a featureType with no existing colourscheme. TODO:
+ * replace return type with object implementing standard abstract colour/style
+ * interface
+ *
+ * @param featureType
+ * @return java.awt.Color or GraduatedColor
+ */
+ public Object getFeatureStyle(String featureType)
{
- if (featureColours.get(featureType) == null)
+ Object fc = featureColours.get(featureType);
+ if (fc == null)
{
- jalview.schemes.UserColourScheme ucs = new
- jalview.schemes.UserColourScheme();
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
Color col = ucs.createColourFromName(featureType);
- featureColours.put(featureType, col);
- return col;
+ featureColours.put(featureType, fc = col);
+ }
+ return fc;
+ }
+
+ /**
+ * return a nominal colour for this feature
+ *
+ * @param featureType
+ * @return standard color, or maximum colour for graduated colourscheme
+ */
+ public Color getColour(String featureType)
+ {
+ Object fc = getFeatureStyle(featureType);
+
+ if (fc instanceof Color)
+ {
+ return (Color) fc;
+ }
+ else
+ {
+ if (fc instanceof GraduatedColor)
+ {
+ return ((GraduatedColor) fc).getMaxColor();
+ }
+ }
+ throw new Error(MessageManager.formatMessage("error.implementation_error_unrecognised_render_object_for_features_type", new String[]{fc.getClass().toString(),featureType}));
+ }
+
+ /**
+ * calculate the render colour for a specific feature using current feature
+ * settings.
+ *
+ * @param feature
+ * @return render colour for the given feature
+ */
+ public Color getColour(SequenceFeature feature)
+ {
+ Object fc = getFeatureStyle(feature.getType());
+ if (fc instanceof Color)
+ {
+ return (Color) fc;
}
else
- return (Color) featureColours.get(featureType);
+ {
+ if (fc instanceof GraduatedColor)
+ {
+ return ((GraduatedColor) fc).findColor(feature);
+ }
+ }
+ throw new Error(MessageManager.formatMessage("error.implementation_error_unrecognised_render_object_for_features_type", new String[]{fc.getClass().toString(),feature.getType()}));
}
+ private boolean showFeature(SequenceFeature sequenceFeature)
+ {
+ Object fc = getFeatureStyle(sequenceFeature.type);
+ if (fc instanceof GraduatedColor)
+ {
+ return ((GraduatedColor) fc).isColored(sequenceFeature);
+ }
+ else
+ {
+ return true;
+ }
+ }
+
+ // // /////////////
+ // // Feature Editing Dialog
+ // // Will be refactored in next release.
+
static String lastFeatureAdded;
+
static String lastFeatureGroupAdded;
+
static String lastDescriptionAdded;
- public boolean createNewFeatures(SequenceI[] sequences,
- SequenceFeature[] features)
- {
- return amendFeatures(sequences, features, true, null);
- }
+ Object oldcol, fcol;
int featureIndex = 0;
+
boolean amendFeatures(final SequenceI[] sequences,
- final SequenceFeature[] features,
- boolean newFeatures,
- final AlignmentPanel ap)
+ final SequenceFeature[] features, boolean newFeatures,
+ final AlignmentPanel ap)
{
- findAllFeatures();
featureIndex = 0;
- JPanel bigPanel = new JPanel(new BorderLayout());
+ final JPanel bigPanel = new JPanel(new BorderLayout());
final JComboBox overlaps;
final JTextField name = new JTextField(25);
final JTextField source = new JTextField(25);
final JSpinner end = new JSpinner();
start.setPreferredSize(new Dimension(80, 20));
end.setPreferredSize(new Dimension(80, 20));
-
- final JPanel colour = new JPanel();
- colour.setBorder(BorderFactory.createEtchedBorder());
- colour.setMaximumSize(new Dimension(40, 10));
+ final FeatureRenderer me = this;
+ final JLabel colour = new JLabel();
+ colour.setOpaque(true);
+ // colour.setBorder(BorderFactory.createEtchedBorder());
+ colour.setMaximumSize(new Dimension(30, 16));
colour.addMouseListener(new MouseAdapter()
{
+ FeatureColourChooser fcc = null;
+
public void mousePressed(MouseEvent evt)
{
- colour.setBackground(
- JColorChooser.showDialog(Desktop.desktop,
- "Select Feature Colour",
- colour.getBackground()));
+ if (fcol instanceof Color)
+ {
+ Color col = JColorChooser.showDialog(Desktop.desktop,
+ MessageManager.getString("label.select_feature_colour"), ((Color) fcol));
+ if (col != null)
+ {
+ fcol = col;
+ updateColourButton(bigPanel, colour, col);
+ }
+ }
+ else
+ {
+
+ if (fcc == null)
+ {
+ final String type = features[featureIndex].getType();
+ fcc = new FeatureColourChooser(me, type);
+ fcc.setRequestFocusEnabled(true);
+ fcc.requestFocus();
+
+ fcc.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ fcol = fcc.getLastColour();
+ fcc = null;
+ setColour(type, fcol);
+ updateColourButton(bigPanel, colour, fcol);
+ }
+ });
+
+ }
+ }
}
});
-
JPanel tmp = new JPanel();
JPanel panel = new JPanel(new GridLayout(3, 1));
- ///////////////////////////////////////
- ///MULTIPLE FEATURES AT SELECTED RESIDUE
- if(!newFeatures && features.length>1)
- {
- panel = new JPanel(new GridLayout(4, 1));
- tmp = new JPanel();
- tmp.add(new JLabel("Select Feature: "));
- overlaps = new JComboBox();
- for(int i=0; i<features.length; i++)
- {
- overlaps.addItem(features[i].getType()
- +"/"+features[i].getBegin()+"-"+features[i].getEnd()
- +" ("+features[i].getFeatureGroup()+")");
- }
-
- tmp.add(overlaps);
-
- overlaps.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent e)
- {
- int index = overlaps.getSelectedIndex();
- if (index != -1)
- {
- featureIndex = index;
- name.setText(features[index].getType());
- description.setText(features[index].getDescription());
- source.setText(features[index].getFeatureGroup());
- start.setValue(new Integer(features[index].getBegin()));
- end.setValue(new Integer(features[index].getEnd()));
-
- SearchResults highlight = new SearchResults();
- highlight.addResult(sequences[0],
- features[index].getBegin(),
- features[index].getEnd());
-
- ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
-
- }
- Color col = getColour(name.getText());
- if (col == null)
- {
- col = new
- jalview.schemes.UserColourScheme()
- .createColourFromName(name.getText());
- }
-
- colour.setBackground(col);
- }
- });
-
-
- panel.add(tmp);
- }
- //////////
- //////////////////////////////////////
+ // /////////////////////////////////////
+ // /MULTIPLE FEATURES AT SELECTED RESIDUE
+ if (!newFeatures && features.length > 1)
+ {
+ panel = new JPanel(new GridLayout(4, 1));
+ tmp = new JPanel();
+ tmp.add(new JLabel(MessageManager.getString("label.select_feature")));
+ overlaps = new JComboBox();
+ for (int i = 0; i < features.length; i++)
+ {
+ overlaps.addItem(features[i].getType() + "/"
+ + features[i].getBegin() + "-" + features[i].getEnd()
+ + " (" + features[i].getFeatureGroup() + ")");
+ }
+
+ tmp.add(overlaps);
+
+ overlaps.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ int index = overlaps.getSelectedIndex();
+ if (index != -1)
+ {
+ featureIndex = index;
+ name.setText(features[index].getType());
+ description.setText(features[index].getDescription());
+ source.setText(features[index].getFeatureGroup());
+ start.setValue(new Integer(features[index].getBegin()));
+ end.setValue(new Integer(features[index].getEnd()));
+
+ SearchResults highlight = new SearchResults();
+ highlight.addResult(sequences[0], features[index].getBegin(),
+ features[index].getEnd());
+
+ ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
+
+ }
+ Object col = getFeatureStyle(name.getText());
+ if (col == null)
+ {
+ col = new jalview.schemes.UserColourScheme()
+ .createColourFromName(name.getText());
+ }
+ oldcol = fcol = col;
+ updateColourButton(bigPanel, colour, col);
+ }
+ });
+
+ panel.add(tmp);
+ }
+ // ////////
+ // ////////////////////////////////////
tmp = new JPanel();
panel.add(tmp);
- tmp.add(new JLabel("Name: ", JLabel.RIGHT));
+ tmp.add(new JLabel(MessageManager.getString("label.name"), JLabel.RIGHT));
tmp.add(name);
tmp = new JPanel();
panel.add(tmp);
- tmp.add(new JLabel("Group: ", JLabel.RIGHT));
+ tmp.add(new JLabel(MessageManager.getString("label.group") + ":",
+ JLabel.RIGHT));
tmp.add(source);
tmp = new JPanel();
panel.add(tmp);
- tmp.add(new JLabel("Colour: ", JLabel.RIGHT));
+ tmp.add(new JLabel(MessageManager.getString("label.colour"),
+ JLabel.RIGHT));
tmp.add(colour);
colour.setPreferredSize(new Dimension(150, 15));
-
+ colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
+ colour.setForeground(Color.black);
+ colour.setHorizontalAlignment(SwingConstants.CENTER);
+ colour.setVerticalAlignment(SwingConstants.CENTER);
+ colour.setHorizontalTextPosition(SwingConstants.CENTER);
+ colour.setVerticalTextPosition(SwingConstants.CENTER);
bigPanel.add(panel, BorderLayout.NORTH);
panel = new JPanel();
- panel.add(new JLabel("Description: ", JLabel.RIGHT));
- description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ panel.add(new JLabel(MessageManager.getString("label.description"),
+ JLabel.RIGHT));
+ description.setFont(JvSwingUtils.getTextAreaFont());
description.setLineWrap(true);
panel.add(new JScrollPane(description));
bigPanel.add(panel, BorderLayout.SOUTH);
panel = new JPanel();
- panel.add(new JLabel(" Start:", JLabel.RIGHT));
+ panel.add(new JLabel(MessageManager.getString("label.start"),
+ JLabel.RIGHT));
panel.add(start);
- panel.add(new JLabel(" End:", JLabel.RIGHT));
+ panel.add(new JLabel(MessageManager.getString("label.end"),
+ JLabel.RIGHT));
panel.add(end);
bigPanel.add(panel, BorderLayout.CENTER);
}
}
}
- name.setText(lastFeatureAdded);
- source.setText(lastFeatureGroupAdded);
+ if (newFeatures)
+ {
+ name.setText(lastFeatureAdded);
+ source.setText(lastFeatureGroupAdded);
+ }
+ else
+ {
+ name.setText(features[0].getType());
+ source.setText(features[0].getFeatureGroup());
+ }
+
start.setValue(new Integer(features[0].getBegin()));
end.setValue(new Integer(features[0].getEnd()));
- colour.setBackground( getColour(lastFeatureAdded) );
description.setText(features[0].getDescription());
-
-
+ updateColourButton(bigPanel, colour,
+ (oldcol = fcol = getFeatureStyle(name.getText())));
Object[] options;
if (!newFeatures)
{
options = new Object[]
- {
- "Amend", "Delete", "Cancel"};
+ { "Amend", "Delete", "Cancel" };
}
else
{
options = new Object[]
- {
- "OK", "Cancel"};
+ { "OK", "Cancel" };
}
- String title = newFeatures ? "Create New Sequence Feature(s)" :
- "Amend/Delete Features for "
- + sequences[0].getName();
+ String title = newFeatures ? MessageManager.getString("label.create_new_sequence_features")
+ : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()});
int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
- bigPanel,
- title,
- JOptionPane.YES_NO_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE,
- null,
- options, "OK");
+ bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
+ JOptionPane.QUESTION_MESSAGE, null, options, MessageManager.getString("action.ok"));
jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
- if (reply == JOptionPane.OK_OPTION
- && name.getText() != null
- && source.getText() != null)
+ if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0)
{
// This ensures that the last sequence
// is refreshed and new features are rendered
lastSeq = null;
- lastFeatureAdded = name.getText();
- lastFeatureGroupAdded = source.getText();
+ lastFeatureAdded = name.getText().trim();
+ lastFeatureGroupAdded = source.getText().trim();
lastDescriptionAdded = description.getText().replaceAll("\n", " ");
+ // TODO: determine if the null feature group is valid
+ if (lastFeatureGroupAdded.length() < 1)
+ lastFeatureGroupAdded = null;
}
if (!newFeatures)
sf.type = lastFeatureAdded;
sf.featureGroup = lastFeatureGroupAdded;
sf.description = lastDescriptionAdded;
- setColour(sf.type, colour.getBackground());
+
+ setColour(sf.type, fcol);
+ av.featuresDisplayed.put(sf.type, getColour(sf.type));
+
try
{
- sf.begin = ( (Integer) start.getValue()).intValue();
- sf.end = ( (Integer) end.getValue()).intValue();
+ sf.begin = ((Integer) start.getValue()).intValue();
+ sf.end = ((Integer) end.getValue()).intValue();
+ } catch (NumberFormatException ex)
+ {
}
- catch (NumberFormatException ex)
- {}
ffile.parseDescriptionHTML(sf, false);
}
}
else
+ // NEW FEATURES ADDED
{
- if (reply == JOptionPane.OK_OPTION
- && name.getText() != null
- && source.getText() != null)
+ if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
{
for (int i = 0; i < sequences.length; i++)
{
features[i].type = lastFeatureAdded;
- features[i].featureGroup = lastFeatureGroupAdded;
+ if (lastFeatureGroupAdded != null)
+ features[i].featureGroup = lastFeatureGroupAdded;
features[i].description = lastDescriptionAdded;
sequences[i].addSequenceFeature(features[i]);
ffile.parseDescriptionHTML(features[i], false);
av.featuresDisplayed = new Hashtable();
}
- if (featureGroups == null)
+ if (lastFeatureGroupAdded != null)
{
- featureGroups = new Hashtable();
+ if (featureGroups == null)
+ featureGroups = new Hashtable();
+ featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
}
+ setColour(lastFeatureAdded, fcol);
+ av.featuresDisplayed.put(lastFeatureAdded,
+ getColour(lastFeatureAdded));
- featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
-
- Color col = colour.getBackground();
- setColour(lastFeatureAdded, colour.getBackground());
-
- av.featuresDisplayed.put(lastFeatureGroupAdded,
- new Integer(col.getRGB()));
+ findAllFeatures(false);
- findAllFeatures();
+ ap.paintAlignment(true);
return true;
}
}
}
- findAllFeatures();
+ ap.paintAlignment(true);
return true;
}
- public void setColour(String featureType, Color col)
+ /**
+ * update the amend feature button dependent on the given style
+ *
+ * @param bigPanel
+ * @param col
+ * @param col2
+ */
+ protected void updateColourButton(JPanel bigPanel, JLabel colour,
+ Object col2)
+ {
+ colour.removeAll();
+ colour.setIcon(null);
+ colour.setToolTipText(null);
+ colour.setText("");
+
+ if (col2 instanceof Color)
+ {
+ colour.setBackground((Color) col2);
+ }
+ else
+ {
+ colour.setBackground(bigPanel.getBackground());
+ colour.setForeground(Color.black);
+ FeatureSettings.renderGraduatedColor(colour, (GraduatedColor) col2);
+ // colour.setForeground(colour.getBackground());
+ }
+ }
+
+ public void setColour(String featureType, Object col)
{
- featureColours.put(featureType, col);
+ // overwrite
+ // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof
+ // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null;
+ // Object c = featureColours.get(featureType);
+ // if (c == null || c instanceof Color || (c instanceof GraduatedColor &&
+ // !((GraduatedColor)c).getMaxColor().equals(_col)))
+ {
+ featureColours.put(featureType, col);
+ }
}
public void setTransparency(float value)
{
return transparency;
}
+
/**
* Replace current ordering with new ordering
- * @param data { String(Type), Colour(Type), Boolean(Displayed) }
+ *
+ * @param data
+ * { String(Type), Colour(Type), Boolean(Displayed) }
*/
public void setFeaturePriority(Object[][] data)
{
setFeaturePriority(data, true);
}
+
/**
- *
- * @param data { String(Type), Colour(Type), Boolean(Displayed) }
- * @param visibleNew when true current featureDisplay list will be cleared
+ *
+ * @param data
+ * { String(Type), Colour(Type), Boolean(Displayed) }
+ * @param visibleNew
+ * when true current featureDisplay list will be cleared
*/
public void setFeaturePriority(Object[][] data, boolean visibleNew)
{
if (visibleNew)
- {
+ {
if (av.featuresDisplayed != null)
{
av.featuresDisplayed.clear();
av.featuresDisplayed = new Hashtable();
}
}
- if (data==null)
+ if (data == null)
{
return;
}
for (int i = 0; i < data.length; i++)
{
String type = data[i][0].toString();
- setColour(type, (Color) data[i][1]);
- if ( ( (Boolean) data[i][2]).booleanValue())
+ setColour(type, data[i][1]); // todo : typesafety - feature color
+ // interface object
+ if (((Boolean) data[i][2]).booleanValue())
{
- av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
+ av.featuresDisplayed.put(type, new Integer(getColour(type)
+ .getRGB()));
}
renderOrder[data.length - i - 1] = type;
}
}
- Hashtable featureOrder=null;
+
+ Map featureOrder = null;
+
/**
* analogous to colour - store a normalized ordering for all feature types in
* this rendering context.
- *
+ *
* @param type
* Feature type string
* @param position
*/
public float setOrder(String type, float position)
{
- if (featureOrder==null)
+ if (featureOrder == null)
{
featureOrder = new Hashtable();
}
featureOrder.put(type, new Float(position));
return position;
}
+
/**
* get the global priority (0 (top) to 1 (bottom))
- *
+ *
* @param type
* @return [0,1] or -1 for a type without a priority
*/
- public float getOrder(String type) {
- if (featureOrder!=null)
+ public float getOrder(String type)
+ {
+ if (featureOrder != null)
{
if (featureOrder.containsKey(type))
{
- return ((Float)featureOrder.get(type)).floatValue();
+ return ((Float) featureOrder.get(type)).floatValue();
}
}
return -1;
git://source.jalview.org / jalview.git / blobdiff