/*
- * 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
+ * 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.
- *
+ * 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/>.
- */
-package jalview.gui;
-
-import java.util.*;
-import java.util.concurrent.ConcurrentHashMap;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import java.beans.PropertyChangeListener;
-import java.beans.PropertyChangeSupport;
-
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.GraduatedColor;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-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;
-
- Map featureColours = new ConcurrentHashMap();
-
- // A higher level for grouping features of a
- // particular type
- 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);
-
- Vector allfeatures;
-
- /**
- * Creates a new FeatureRenderer object.
- *
- * @param av
- * DOCUMENT ME!
- */
- public FeatureRenderer(AlignmentPanel ap)
- {
- this.ap = ap;
- this.av = ap.av;
- }
-
- 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;
- }
-
- public void transferSettings(FeatureRenderer fr)
- {
- 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));
- }
-
- /**
- * This is used by the Molecule Viewer and Overview to get the accurate
- * colourof the rendered sequence
- */
- public synchronized int findFeatureColour(int initialCol, SequenceI seq,
- int column)
- {
- if (!av.showSequenceFeatures)
- {
- return initialCol;
- }
-
- if (seq != lastSeq)
- {
- lastSeq = seq;
- sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
- if (sequenceFeatures != null)
- {
- sfSize = sequenceFeatures.length;
- }
- }
-
- if (sequenceFeatures != lastSeq.getDatasetSequence()
- .getSequenceFeatures())
- {
- sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
- if (sequenceFeatures != null)
- {
- sfSize = sequenceFeatures.length;
- }
- }
-
- if (sequenceFeatures == null || sfSize == 0)
- {
- return initialCol;
- }
-
- if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
- {
- return Color.white.getRGB();
- }
-
- // Only bother making an offscreen image if transparency is applied
- if (transparency != 1.0f && offscreenImage == null)
- {
- offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);
- }
-
- 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);
-
- return offscreenImage.getRGB(0, 0);
- }
- else
- {
- drawSequence(null, lastSeq, lastSeq.findPosition(column), -1, -1);
-
- if (currentColour == null)
- {
- return initialCol;
- }
- else
- {
- return ((Integer) currentColour).intValue();
- }
- }
-
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g
- * DOCUMENT ME!
- * @param seq
- * DOCUMENT ME!
- * @param sg
- * DOCUMENT ME!
- * @param start
- * DOCUMENT ME!
- * @param end
- * DOCUMENT ME!
- * @param x1
- * DOCUMENT ME!
- * @param y1
- * DOCUMENT ME!
- * @param width
- * DOCUMENT ME!
- * @param height
- * DOCUMENT ME!
- */
- // String type;
- // SequenceFeature sf;
- SequenceI lastSeq;
-
- SequenceFeature[] sequenceFeatures;
-
- int sfSize, sfindex, spos, epos;
-
- /**
- * 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)
- {
- return;
- }
-
- if (g != null)
- {
- fm = g.getFontMetrics();
- }
-
- if (av.featuresDisplayed == null || renderOrder == null
- || newFeatureAdded)
- {
- findAllFeatures();
- if (av.featuresDisplayed.size() < 1)
- {
- return;
- }
-
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
- }
-
- if (lastSeq == null
- || seq != lastSeq
- || seq.getDatasetSequence().getSequenceFeatures() != sequenceFeatures)
- {
- lastSeq = seq;
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
- }
-
- if (transparency != 1 && g != null)
- {
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
- transparency));
- }
-
- if (!offscreenRender)
- {
- spos = lastSeq.findPosition(start);
- epos = lastSeq.findPosition(end);
- }
-
- sfSize = sequenceFeatures.length;
- String type;
- for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
- {
- type = renderOrder[renderIndex];
-
- if (type == null || !av.featuresDisplayed.containsKey(type))
- {
- continue;
- }
-
- // loop through all features in sequence to find
- // current feature to render
- for (sfindex = 0; sfindex < sfSize; sfindex++)
- {
- if (!sequenceFeatures[sfindex].type.equals(type))
- {
- continue;
- }
-
- if (featureGroups != null
- && 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))
- {
- continue;
- }
-
- if (offscreenRender && offscreenImage == null)
- {
- if (sequenceFeatures[sfindex].begin <= start
- && sequenceFeatures[sfindex].end >= start)
- {
- // 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,
- 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,
- getColour(sequenceFeatures[sfindex])
- // new Color(((Integer) av.featuresDisplayed
- // .get(sequenceFeatures[sfindex].type)).intValue())
- , start, end, y1);
-
- }
- else if (showFeature(sequenceFeatures[sfindex]))
- {
- 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));
- }
- }
-
- 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)
- {
-
- 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;
- for (i = fstart; i <= fend; i++)
- {
- s = seq.getCharAt(i);
-
- if (jalview.util.Comparison.isGap(s))
- {
- continue;
- }
-
- g.setColor(featureColour);
-
- g.fillRect((i - start) * av.charWidth, y1, av.charWidth,
- av.charHeight);
-
- if (offscreenRender || !av.validCharWidth)
- {
- continue;
- }
-
- g.setColor(Color.white);
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- 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.
- *
- */
- public void featuresAdded()
- {
- 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.
- *
- */
- void findAllFeatures()
- {
- 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)
- {
- newFeatureAdded = false;
-
- if (findingFeatures)
- {
- newFeatureAdded = true;
- return;
- }
-
- findingFeatures = true;
-
- if (av.featuresDisplayed == null)
- {
- av.featuresDisplayed = new Hashtable();
- }
-
- allfeatures = new Vector();
- Vector oldfeatures = new Vector();
- if (renderOrder != null)
- {
- for (int i = 0; i < renderOrder.length; i++)
- {
- if (renderOrder[i] != null)
- {
- oldfeatures.addElement(renderOrder[i]);
- }
- }
- }
- if (minmax == null)
- {
- minmax = new Hashtable();
- }
- AlignmentI alignment = av.getAlignment();
- for (int i = 0; i < alignment.getHeight(); i++)
- {
- SequenceFeature[] features = alignment.getSequenceAt(i)
- .getDatasetSequence().getSequenceFeatures();
-
- if (features == null)
- {
- continue;
- }
-
- int index = 0;
- while (index < features.length)
- {
- if (!av.featuresDisplayed.containsKey(features[index].getType()))
- {
-
- if (featureGroups.containsKey(features[index].getType()))
- {
- boolean visible = ((Boolean) featureGroups
- .get(features[index].featureGroup)).booleanValue();
+ * 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.gui;
- if (!visible)
- {
- index++;
- continue;
- }
- }
+import jalview.api.FeatureColourI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.FeaturesFile;
+import jalview.schemes.FeatureColour;
+import jalview.util.ColorUtils;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.List;
+
+import javax.swing.JColorChooser;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSpinner;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
- 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
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FeatureRenderer
+ extends jalview.renderer.seqfeatures.FeatureRenderer
+{
+ /*
+ * defaults for creating a new feature are the last created
+ * feature type and group
+ */
+ static String lastFeatureAdded = "feature_1";
- 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);
- }
- }
- }
- 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 };
+ static String lastFeatureGroupAdded = "Jalview";
- }
- 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;
- }
+ Color resBoxColour;
- protected Boolean firing = Boolean.FALSE;
+ AlignmentPanel ap;
/**
- * 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
+ * Creates a new FeatureRenderer object
*
- * @param allFeatures
+ * @param alignPanel
*/
- private void updateRenderOrder(Vector allFeatures)
+ public FeatureRenderer(AlignmentPanel alignPanel)
{
- Vector allfeatures = new Vector(allFeatures);
- String[] oldRender = renderOrder;
- renderOrder = new String[allfeatures.size()];
- 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++)
- {
- if (oldRender[j] != null)
- {
- 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)
- {
- 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)
- {
- // no new features - leave order unchanged.
- return;
- }
- 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();
- // sort remaining 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);
- }
- // set order from newly found feature from persisted ordering.
- 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];
- }
- i--;
- }
- if (iSize > 1 && sort)
+ super(alignPanel.av);
+ this.ap = alignPanel;
+ if (alignPanel.getSeqPanel() != null
+ && alignPanel.getSeqPanel().seqCanvas != null
+ && alignPanel.getSeqPanel().seqCanvas.fr != null)
{
- jalview.util.QuickSort.sort(sortOrder, newf);
+ transferSettings(alignPanel.getSeqPanel().seqCanvas.fr);
}
- sortOrder = null;
- System.arraycopy(newf, 0, renderOrder, opos, newf.length);
}
- /**
- * 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)
- {
- Object fc = featureColours.get(featureType);
- if (fc == null)
- {
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
- Color col = ucs.createColourFromName(featureType);
- featureColours.put(featureType, fc = col);
- }
- return fc;
- }
+ FeatureColourI oldcol, fcol;
+
+ int featureIndex = 0;
/**
- * return a nominal colour for this feature
+ * Presents a dialog allowing the user to add new features, or amend or delete
+ * existing features. Currently this can be on
+ * <ul>
+ * <li>double-click on a sequence - Amend/Delete features at position</li>
+ * <li>Create sequence feature from pop-up menu on selected region</li>
+ * <li>Create features for pattern matches from Find</li>
+ * </ul>
+ * If the supplied feature type is null, show (and update on confirm) the type
+ * and group of the last new feature created (with initial defaults of
+ * "feature_1" and "Jalview").
*
- * @param featureType
- * @return standard color, or maximum colour for graduated colourscheme
+ * @param sequences
+ * the sequences features are to be created on (if creating
+ * features), or a single sequence (if amending features)
+ * @param features
+ * the current features at the position (if amending), or template
+ * new feature(s) with start/end position set (if creating)
+ * @param create
+ * true to create features, false to amend or delete
+ * @param alignPanel
+ * @return
*/
- public Color getColour(String featureType)
+ protected boolean amendFeatures(final List<SequenceI> sequences,
+ final List<SequenceFeature> features, boolean create,
+ final AlignmentPanel alignPanel)
{
- Object fc = getFeatureStyle(featureType);
+ featureIndex = 0;
- if (fc instanceof Color)
- {
- return (Color) fc;
- }
- else
+ final JPanel mainPanel = new JPanel(new BorderLayout());
+
+ final JTextField name = new JTextField(25);
+ name.getDocument().addDocumentListener(new DocumentListener()
{
- if (fc instanceof GraduatedColor)
+ @Override
+ public void insertUpdate(DocumentEvent e)
{
- return ((GraduatedColor) fc).getMaxColor();
+ warnIfTypeHidden(mainPanel, name.getText());
}
- }
- throw new Error("Implementation Error: Unrecognised render object "
- + fc.getClass() + " for features of type " + 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
- {
- if (fc instanceof GraduatedColor)
+ @Override
+ public void removeUpdate(DocumentEvent e)
{
- return ((GraduatedColor) fc).findColor(feature);
+ warnIfTypeHidden(mainPanel, name.getText());
}
- }
- throw new Error("Implementation Error: Unrecognised render object "
- + fc.getClass() + " for features of type " + 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;
-
- Object oldcol, fcol;
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ warnIfTypeHidden(mainPanel, name.getText());
+ }
+ });
- int featureIndex = 0;
+ final JTextField group = new JTextField(25);
+ group.getDocument().addDocumentListener(new DocumentListener()
+ {
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ warnIfGroupHidden(mainPanel, group.getText());
+ }
- boolean amendFeatures(final SequenceI[] sequences,
- final SequenceFeature[] features, boolean newFeatures,
- final AlignmentPanel ap)
- {
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ warnIfGroupHidden(mainPanel, group.getText());
+ }
- featureIndex = 0;
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ warnIfGroupHidden(mainPanel, group.getText());
+ }
+ });
- final JPanel bigPanel = new JPanel(new BorderLayout());
- final JComboBox overlaps;
- final JTextField name = new JTextField(25);
- final JTextField source = new JTextField(25);
final JTextArea description = new JTextArea(3, 25);
final JSpinner start = new JSpinner();
final JSpinner end = new JSpinner();
start.setPreferredSize(new Dimension(80, 20));
end.setPreferredSize(new Dimension(80, 20));
- 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;
-
+ /*
+ * open colour chooser on click in colour panel
+ */
+ @Override
public void mousePressed(MouseEvent evt)
{
- if (fcol instanceof Color)
+ if (fcol.isSimpleColour())
{
Color col = JColorChooser.showDialog(Desktop.desktop,
- "Select Feature Colour", ((Color) fcol));
+ MessageManager.getString("label.select_feature_colour"),
+ fcol.getColour());
if (col != null)
{
- fcol = col;
- updateColourButton(bigPanel, colour, col);
+ fcol = new FeatureColour(col);
+ updateColourButton(mainPanel, colour, fcol);
}
}
else
{
-
- if (fcc == null)
+ /*
+ * variable colour dialog - on OK, refetch the updated
+ * feature colour and update this display
+ */
+ final String ft = features.get(featureIndex).getType();
+ final String type = ft == null ? lastFeatureAdded : ft;
+ FeatureTypeSettings fcc = new FeatureTypeSettings(
+ FeatureRenderer.this, type);
+ fcc.setRequestFocusEnabled(true);
+ fcc.requestFocus();
+ fcc.addActionListener(new ActionListener()
{
- final String type = features[featureIndex].getType();
- fcc = new FeatureColourChooser(me, type);
- fcc.setRequestFocusEnabled(true);
- fcc.requestFocus();
-
- fcc.addActionListener(new ActionListener()
+ @Override
+ public void actionPerformed(ActionEvent e)
{
-
- public void actionPerformed(ActionEvent e)
- {
- fcol = fcc.getLastColour();
- fcc = null;
- setColour(type, fcol);
- updateColourButton(bigPanel, colour, fcol);
- }
- });
-
- }
+ fcol = FeatureRenderer.this.getFeatureStyle(ft);
+ setColour(type, fcol);
+ updateColourButton(mainPanel, 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() + ")");
+ JPanel gridPanel = new JPanel(new GridLayout(3, 1));
+
+ if (!create && features.size() > 1)
+ {
+ /*
+ * more than one feature at selected position -
+ * add a drop-down to choose the feature to amend
+ * space pad text if necessary to make entries distinct
+ */
+ gridPanel = new JPanel(new GridLayout(4, 1));
+ JPanel choosePanel = new JPanel();
+ choosePanel.add(new JLabel(
+ MessageManager.getString("label.select_feature") + ":"));
+ final JComboBox<String> overlaps = new JComboBox<>();
+ List<String> added = new ArrayList<>();
+ for (SequenceFeature sf : features)
+ {
+ String text = String.format("%s/%d-%d (%s)", sf.getType(),
+ sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
+ while (added.contains(text))
+ {
+ text += " ";
+ }
+ overlaps.addItem(text);
+ added.add(text);
}
-
- tmp.add(overlaps);
+ choosePanel.add(overlaps);
overlaps.addItemListener(new ItemListener()
{
+ @Override
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);
-
+ SequenceFeature sf = features.get(index);
+ name.setText(sf.getType());
+ description.setText(sf.getDescription());
+ group.setText(sf.getFeatureGroup());
+ start.setValue(new Integer(sf.getBegin()));
+ end.setValue(new Integer(sf.getEnd()));
+
+ SearchResultsI highlight = new SearchResults();
+ highlight.addResult(sequences.get(0), sf.getBegin(),
+ sf.getEnd());
+
+ alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(
+ highlight, false);
}
- Object col = getFeatureStyle(name.getText());
+ FeatureColourI col = getFeatureStyle(name.getText());
if (col == null)
{
- col = new jalview.schemes.UserColourScheme()
- .createColourFromName(name.getText());
+ col = new FeatureColour(
+ ColorUtils.createColourFromName(name.getText()));
}
oldcol = fcol = col;
- updateColourButton(bigPanel, colour, col);
+ updateColourButton(mainPanel, colour, col);
}
});
- panel.add(tmp);
+ gridPanel.add(choosePanel);
}
- // ////////
- // ////////////////////////////////////
- tmp = new JPanel();
- panel.add(tmp);
- tmp.add(new JLabel("Name: ", JLabel.RIGHT));
- tmp.add(name);
+ JPanel namePanel = new JPanel();
+ gridPanel.add(namePanel);
+ namePanel.add(new JLabel(MessageManager.getString("label.name:"),
+ JLabel.RIGHT));
+ namePanel.add(name);
- tmp = new JPanel();
- panel.add(tmp);
- tmp.add(new JLabel("Group: ", JLabel.RIGHT));
- tmp.add(source);
+ JPanel groupPanel = new JPanel();
+ gridPanel.add(groupPanel);
+ groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
+ JLabel.RIGHT));
+ groupPanel.add(group);
- tmp = new JPanel();
- panel.add(tmp);
- tmp.add(new JLabel("Colour: ", JLabel.RIGHT));
- tmp.add(colour);
+ JPanel colourPanel = new JPanel();
+ gridPanel.add(colourPanel);
+ colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
+ JLabel.RIGHT));
+ colourPanel.add(colour);
colour.setPreferredSize(new Dimension(150, 15));
colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
colour.setForeground(Color.black);
colour.setVerticalAlignment(SwingConstants.CENTER);
colour.setHorizontalTextPosition(SwingConstants.CENTER);
colour.setVerticalTextPosition(SwingConstants.CENTER);
- bigPanel.add(panel, BorderLayout.NORTH);
+ mainPanel.add(gridPanel, BorderLayout.NORTH);
- panel = new JPanel();
- panel.add(new JLabel("Description: ", JLabel.RIGHT));
+ JPanel descriptionPanel = new JPanel();
+ descriptionPanel.add(new JLabel(
+ MessageManager.getString("label.description:"), JLabel.RIGHT));
description.setFont(JvSwingUtils.getTextAreaFont());
description.setLineWrap(true);
- panel.add(new JScrollPane(description));
-
- if (!newFeatures)
- {
- bigPanel.add(panel, BorderLayout.SOUTH);
-
- panel = new JPanel();
- panel.add(new JLabel(" Start:", JLabel.RIGHT));
- panel.add(start);
- panel.add(new JLabel(" End:", JLabel.RIGHT));
- panel.add(end);
- bigPanel.add(panel, BorderLayout.CENTER);
- }
- else
- {
- bigPanel.add(panel, BorderLayout.CENTER);
- }
+ descriptionPanel.add(new JScrollPane(description));
- if (lastFeatureAdded == null)
+ if (!create)
{
- if (features[0].type != null)
- {
- lastFeatureAdded = features[0].type;
- }
- else
- {
- lastFeatureAdded = "feature_1";
- }
- }
-
- if (lastFeatureGroupAdded == null)
- {
- if (features[0].featureGroup != null)
- {
- lastFeatureGroupAdded = features[0].featureGroup;
- }
- else
- {
- lastFeatureGroupAdded = "Jalview";
- }
- }
+ mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
- if (newFeatures)
- {
- name.setText(lastFeatureAdded);
- source.setText(lastFeatureGroupAdded);
+ JPanel startEndPanel = new JPanel();
+ startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
+ JLabel.RIGHT));
+ startEndPanel.add(start);
+ startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
+ JLabel.RIGHT));
+ startEndPanel.add(end);
+ mainPanel.add(startEndPanel, BorderLayout.CENTER);
}
else
{
- name.setText(features[0].getType());
- source.setText(features[0].getFeatureGroup());
+ mainPanel.add(descriptionPanel, BorderLayout.CENTER);
}
- start.setValue(new Integer(features[0].getBegin()));
- end.setValue(new Integer(features[0].getEnd()));
- description.setText(features[0].getDescription());
- updateColourButton(bigPanel, colour,
- (oldcol = fcol = getFeatureStyle(name.getText())));
+ /*
+ * default feature type and group to that of the first feature supplied,
+ * or to the last feature created if not supplied (null value)
+ */
+ SequenceFeature firstFeature = features.get(0);
+ boolean useLastDefaults = firstFeature.getType() == null;
+ final String featureType = useLastDefaults ? lastFeatureAdded
+ : firstFeature.getType();
+ final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
+ : firstFeature.getFeatureGroup();
+ name.setText(featureType);
+ group.setText(featureGroup);
+
+ start.setValue(new Integer(firstFeature.getBegin()));
+ end.setValue(new Integer(firstFeature.getEnd()));
+ description.setText(firstFeature.getDescription());
+ updateColourButton(mainPanel, colour,
+ (oldcol = fcol = getFeatureStyle(featureType)));
Object[] options;
- if (!newFeatures)
+ if (!create)
{
- options = new Object[]
- { "Amend", "Delete", "Cancel" };
+ options = new Object[] { MessageManager.getString("label.amend"),
+ MessageManager.getString("action.delete"),
+ MessageManager.getString("action.cancel") };
}
else
{
- options = new Object[]
- { "OK", "Cancel" };
+ options = new Object[] { MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") };
}
- String title = newFeatures ? "Create New Sequence Feature(s)"
- : "Amend/Delete Features for " + sequences[0].getName();
+ String title = create
+ ? MessageManager.getString("label.create_new_sequence_features")
+ : MessageManager.formatMessage("label.amend_delete_features",
+ new String[]
+ { sequences.get(0).getName() });
- int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
- bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE, null, options, "OK");
+ /*
+ * show the dialog
+ */
+ int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
+ mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
+ JvOptionPane.QUESTION_MESSAGE, null, options,
+ MessageManager.getString("action.ok"));
+
+ FeaturesFile ffile = new FeaturesFile();
- jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+ final String enteredType = name.getText().trim();
+ final String enteredGroup = group.getText().trim();
+ final String enteredDescription = description.getText().replaceAll("\n", " ");
- if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0)
+ if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
{
- // This ensures that the last sequence
- // is refreshed and new features are rendered
- lastSeq = null;
- 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;
+ /*
+ * update default values only if creating using default values
+ */
+ if (useLastDefaults)
+ {
+ lastFeatureAdded = enteredType;
+ lastFeatureGroupAdded = enteredGroup;
+ // TODO: determine if the null feature group is valid
+ if (lastFeatureGroupAdded.length() < 1)
+ {
+ lastFeatureGroupAdded = null;
+ }
+ }
}
- if (!newFeatures)
+ if (!create)
{
- SequenceFeature sf = features[featureIndex];
+ SequenceFeature sf = features.get(featureIndex);
- if (reply == JOptionPane.NO_OPTION)
+ if (reply == JvOptionPane.NO_OPTION)
{
- sequences[0].getDatasetSequence().deleteFeature(sf);
+ /*
+ * NO_OPTION corresponds to the Delete button
+ */
+ sequences.get(0).getDatasetSequence().deleteFeature(sf);
+ // update Feature Settings for removal of feature / group
+ featuresAdded();
}
- else if (reply == JOptionPane.YES_OPTION)
+ else if (reply == JvOptionPane.YES_OPTION)
{
- sf.type = lastFeatureAdded;
- sf.featureGroup = lastFeatureGroupAdded;
- sf.description = lastDescriptionAdded;
-
- setColour(sf.type, fcol);
- av.featuresDisplayed.put(sf.type, getColour(sf.type));
-
+ /*
+ * YES_OPTION corresponds to the Amend button
+ * need to refresh Feature Settings if type, group or colour changed;
+ * note we don't force the feature to be visible - the user has been
+ * warned if a hidden feature type or group was entered
+ */
+ boolean refreshSettings = (!featureType.equals(enteredType) || !featureGroup
+ .equals(enteredGroup));
+ refreshSettings |= (fcol != oldcol);
+ setColour(enteredType, fcol);
+ int newBegin = sf.begin;
+ int newEnd = sf.end;
try
{
- sf.begin = ((Integer) start.getValue()).intValue();
- sf.end = ((Integer) end.getValue()).intValue();
+ newBegin = ((Integer) start.getValue()).intValue();
+ newEnd = ((Integer) end.getValue()).intValue();
} catch (NumberFormatException ex)
{
+ // JSpinner doesn't accept invalid format data :-)
}
- ffile.parseDescriptionHTML(sf, false);
+ /*
+ * replace the feature by deleting it and adding a new one
+ * (to ensure integrity of SequenceFeatures data store)
+ */
+ sequences.get(0).deleteFeature(sf);
+ SequenceFeature newSf = new SequenceFeature(sf, enteredType,
+ newBegin, newEnd, enteredGroup, sf.getScore());
+ newSf.setDescription(enteredDescription);
+ ffile.parseDescriptionHTML(newSf, false);
+ // amend features dialog only updates one sequence at a time
+ sequences.get(0).addSequenceFeature(newSf);
+
+ if (refreshSettings)
+ {
+ featuresAdded();
+ }
}
}
else
// NEW FEATURES ADDED
{
- if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
+ if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
{
- for (int i = 0; i < sequences.length; i++)
- {
- features[i].type = lastFeatureAdded;
- if (lastFeatureGroupAdded != null)
- features[i].featureGroup = lastFeatureGroupAdded;
- features[i].description = lastDescriptionAdded;
- sequences[i].addSequenceFeature(features[i]);
- ffile.parseDescriptionHTML(features[i], false);
- }
-
- if (av.featuresDisplayed == null)
+ for (int i = 0; i < sequences.size(); i++)
{
- av.featuresDisplayed = new Hashtable();
+ SequenceFeature sf = features.get(i);
+ SequenceFeature sf2 = new SequenceFeature(enteredType,
+ enteredDescription, sf.getBegin(), sf.getEnd(),
+ enteredGroup);
+ ffile.parseDescriptionHTML(sf2, false);
+ sequences.get(i).addSequenceFeature(sf2);
}
- if (lastFeatureGroupAdded != null)
- {
- if (featureGroups == null)
- featureGroups = new Hashtable();
- featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
- }
- setColour(lastFeatureAdded, fcol);
- av.featuresDisplayed.put(lastFeatureAdded,
- getColour(lastFeatureAdded));
+ setColour(enteredType, fcol);
- findAllFeatures(false);
+ featuresAdded();
- ap.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
return true;
}
}
}
- ap.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
return true;
}
/**
- * 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)
- {
- // 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)
- {
- transparency = value;
- }
-
- public float getTransparency()
- {
- return transparency;
- }
-
- /**
- * Replace current ordering with new ordering
+ * Show a warning message if the entered type is one that is currently hidden
*
- * @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 panel
+ * @param type
*/
- public void setFeaturePriority(Object[][] data, boolean visibleNew)
+ protected void warnIfTypeHidden(JPanel panel, String type)
{
- if (visibleNew)
- {
- if (av.featuresDisplayed != null)
- {
- av.featuresDisplayed.clear();
- }
- else
- {
- av.featuresDisplayed = new Hashtable();
- }
- }
- if (data == null)
- {
- return;
- }
-
- // The feature table will display high priority
- // features at the top, but theses are the ones
- // we need to render last, so invert the data
- renderOrder = new String[data.length];
-
- if (data.length > 0)
+ if (getRenderOrder().contains(type))
{
- for (int i = 0; i < data.length; i++)
+ if (!showFeatureOfType(type))
{
- String type = data[i][0].toString();
- 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()));
- }
-
- renderOrder[data.length - i - 1] = type;
+ String msg = MessageManager.formatMessage("label.warning_hidden",
+ MessageManager.getString("label.feature_type"), type);
+ JvOptionPane.showMessageDialog(panel, msg, "",
+ JvOptionPane.OK_OPTION);
}
}
-
}
- Map featureOrder = null;
-
/**
- * analogous to colour - store a normalized ordering for all feature types in
- * this rendering context.
+ * Show a warning message if the entered group is one that is currently hidden
*
- * @param type
- * Feature type string
- * @param position
- * normalized priority - 0 means always appears on top, 1 means
- * always last.
+ * @param panel
+ * @param group
*/
- public float setOrder(String type, float position)
+ protected void warnIfGroupHidden(JPanel panel, String group)
{
- if (featureOrder == null)
+ if (featureGroups.containsKey(group) && !featureGroups.get(group))
{
- featureOrder = new Hashtable();
+ String msg = MessageManager.formatMessage("label.warning_hidden",
+ MessageManager.getString("label.group"), group);
+ JvOptionPane.showMessageDialog(panel, msg, "",
+ JvOptionPane.OK_OPTION);
}
- featureOrder.put(type, new Float(position));
- return position;
}
/**
- * get the global priority (0 (top) to 1 (bottom))
+ * update the amend feature button dependent on the given style
*
- * @param type
- * @return [0,1] or -1 for a type without a priority
+ * @param bigPanel
+ * @param col
+ * @param col
*/
- public float getOrder(String type)
+ protected void updateColourButton(JPanel bigPanel, JLabel colour,
+ FeatureColourI col)
{
- if (featureOrder != null)
+ colour.removeAll();
+ colour.setIcon(null);
+ colour.setToolTipText(null);
+ colour.setText("");
+
+ if (col.isSimpleColour())
{
- if (featureOrder.containsKey(type))
- {
- return ((Float) featureOrder.get(type)).floatValue();
- }
+ colour.setBackground(col.getColour());
+ }
+ else
+ {
+ colour.setBackground(bigPanel.getBackground());
+ colour.setForeground(Color.black);
+ FeatureSettings.renderGraduatedColor(colour, col);
}
- return -1;
- }
-
- /**
- * @param listener
- * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
- */
- public void addPropertyChangeListener(PropertyChangeListener listener)
- {
- changeSupport.addPropertyChangeListener(listener);
}
/**
- * @param listener
- * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
+ * Orders features in render precedence (last in order is last to render, so
+ * displayed on top of other features)
+ *
+ * @param order
*/
- public void removePropertyChangeListener(PropertyChangeListener listener)
+ public void orderFeatures(Comparator<String> order)
{
- changeSupport.removePropertyChangeListener(listener);
+ Arrays.sort(renderOrder, order);
}
}
git://source.jalview.org / jalview.git / blobdiff