/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
* 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.
- *
+ *
* 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
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
public class FeatureRenderer
{
AlignmentPanel ap;
+
AlignViewport av;
+
Color resBoxColour;
+
float transparency = 1.0f;
+
FontMetrics fm;
+
int charOffset;
Hashtable featureColours = new Hashtable();
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!
+ * DOCUMENT ME!
*/
public FeatureRenderer(AlignmentPanel ap)
{
this.av = ap.av;
}
- public class FeatureRendererSettings implements Cloneable {
+ public class FeatureRendererSettings implements Cloneable
+ {
String[] renderOrder;
+
Hashtable featureGroups;
+
Hashtable featureColours;
+
float transparency;
+
Hashtable featureOrder;
+
public FeatureRendererSettings(String[] renderOrder,
Hashtable featureGroups, Hashtable featureColours,
float transparency, Hashtable featureOrder)
this.transparency = transparency;
this.featureOrder = featureOrder;
}
+
public FeatureRendererSettings(FeatureRenderer fr)
{
this.renderOrder = fr.renderOrder;
this.featureOrder = fr.featureOrder;
}
}
+
public FeatureRendererSettings getSettings()
{
return new FeatureRendererSettings(this);
}
+
public void transferSettings(FeatureRendererSettings fr)
{
this.renderOrder = fr.renderOrder;
this.transparency = fr.transparency;
this.featureOrder = fr.featureOrder;
}
+
public void transferSettings(FeatureRenderer fr)
{
this.renderOrder = fr.renderOrder;
}
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));
}
/**
{
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 || sfSize==0)
+ if (sequenceFeatures == null || sfSize == 0)
{
return initialCol;
}
-
if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
{
return Color.white.getRGB();
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!
+ * DOCUMENT ME!
* @param seq
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param sg
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param start
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param end
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param x1
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param y1
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param width
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param height
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
// String type;
// SequenceFeature sf;
SequenceI lastSeq;
+
SequenceFeature[] sequenceFeatures;
+
int sfSize, sfindex, spos, epos;
synchronized public void drawSequence(Graphics g, SequenceI seq,
- int start, int end, int y1)
+ 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();
}
- if (lastSeq == null || seq != lastSeq
- || seq.getDatasetSequence().getSequenceFeatures()!=sequenceFeatures)
+ 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));
+ g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
+ transparency));
}
if (!offscreenRender)
}
if (featureGroups != null
- && sequenceFeatures[sfindex].featureGroup != null
- &&
- sequenceFeatures[sfindex].featureGroup.length()!=0
- && 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);
+ 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);
- 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);
+ 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);
+ 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);
}
else
{
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex].type),
- start, end, y1);
+ renderFeature(g, seq, seq
+ .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
+ .findIndex(sequenceFeatures[sfindex].end) - 1,
+ getColour(sequenceFeatures[sfindex].type), 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));
}
}
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);
}
}
}
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.
- *
+ *
*/
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;
+ 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
+ * 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++)
{
- SequenceFeature[] features
- = av.alignment.getSequenceAt(i).getDatasetSequence().
- getSequenceFeatures();
+ SequenceFeature[] features = av.alignment.getSequenceAt(i)
+ .getDatasetSequence().getSequenceFeatures();
if (features == null)
{
if (!av.featuresDisplayed.containsKey(features[index].getType()))
{
- if(featureGroups.containsKey(features[index].getType()))
+ if (featureGroups.containsKey(features[index].getType()))
{
- boolean visible = ( (Boolean) featureGroups.get(
- features[index].featureGroup)).booleanValue();
+ boolean visible = ((Boolean) featureGroups
+ .get(features[index].featureGroup)).booleanValue();
- if(!visible)
+ if (!visible)
{
index++;
continue;
}
}
-
- if (! (features[index].begin == 0 && features[index].end == 0))
+ 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()))
{
updateRenderOrder(allfeatures);
findingFeatures = false;
}
- protected Boolean firing=Boolean.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
- *
+ *
* @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)
+ 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]);
- }
+ 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 (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();
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)
{
if (!featureColours.containsKey(featureType))
{
- 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;
}
static String lastFeatureAdded;
+
static String lastFeatureGroupAdded;
+
static String lastDescriptionAdded;
int featureIndex = 0;
+
boolean amendFeatures(final SequenceI[] sequences,
- final SequenceFeature[] features,
- boolean newFeatures,
- final AlignmentPanel ap)
+ final SequenceFeature[] features, boolean newFeatures,
+ final AlignmentPanel ap)
{
featureIndex = 0;
public void mousePressed(MouseEvent evt)
{
Color col = JColorChooser.showDialog(Desktop.desktop,
- "Select Feature Colour",
- colour.getBackground());
+ "Select Feature Colour", colour.getBackground());
if (col != null)
colour.setBackground(col);
JPanel tmp = new JPanel();
JPanel panel = new JPanel(new GridLayout(3, 1));
- ///////////////////////////////////////
- ///MULTIPLE FEATURES AT SELECTED RESIDUE
- if(!newFeatures && features.length>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);
+ 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);
}
- //////////
- //////////////////////////////////////
+ // ////////
+ // ////////////////////////////////////
tmp = new JPanel();
panel.add(tmp);
}
}
- if(newFeatures)
+ if (newFeatures)
{
name.setText(lastFeatureAdded);
source.setText(lastFeatureGroupAdded);
description.setText(features[0].getDescription());
colour.setBackground(getColour(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 ? "Create New Sequence Feature(s)"
+ : "Amend/Delete Features for " + 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, "OK");
jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
- if (reply == JOptionPane.OK_OPTION && name.getText().length()>0)
+ if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0)
{
// This ensures that the last sequence
// is refreshed and new features are rendered
lastFeatureGroupAdded = source.getText().trim();
lastDescriptionAdded = description.getText().replaceAll("\n", " ");
- if(lastFeatureGroupAdded.length()<1)
+ if (lastFeatureGroupAdded.length() < 1)
lastFeatureGroupAdded = null;
}
sf.description = lastDescriptionAdded;
setColour(sf.type, colour.getBackground());
- av.featuresDisplayed.put(sf.type,
- new Integer(colour.getBackground().getRGB()));
+ av.featuresDisplayed.put(sf.type, new Integer(colour
+ .getBackground().getRGB()));
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
+ else
+ // NEW FEATURES ADDED
{
- if (reply == JOptionPane.OK_OPTION
- && lastFeatureAdded.length()>0)
+ if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
{
for (int i = 0; i < sequences.length; i++)
{
features[i].type = lastFeatureAdded;
- if (lastFeatureGroupAdded!=null)
+ if (lastFeatureGroupAdded != null)
features[i].featureGroup = lastFeatureGroupAdded;
features[i].description = lastDescriptionAdded;
sequences[i].addSequenceFeature(features[i]);
Color col = colour.getBackground();
setColour(lastFeatureAdded, colour.getBackground());
av.featuresDisplayed.put(lastFeatureAdded,
- new Integer(col.getRGB()));
+ new Integer(col.getRGB()));
findAllFeatures(false);
ap.paintAlignment(true);
-
return true;
}
else
{
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;
}
{
String type = data[i][0].toString();
setColour(type, (Color) data[i][1]);
- if ( ( (Boolean) data[i][2]).booleanValue())
+ 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;
+
+ Hashtable featureOrder = null;
+
/**
* analogous to colour - store a normalized ordering for all feature types in
* this rendering context.
- *
+ *
* @param type
- * Feature type string
+ * Feature type string
* @param position
- * normalized priority - 0 means always appears on top, 1 means
- * always last.
+ * normalized priority - 0 means always appears on top, 1 means
+ * always last.
*/
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