From 9c8561a294fb638ae78c01a440a863b05db2bdee Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 10 Oct 2007 13:48:26 +0000 Subject: [PATCH] featureGroup show/hide and newView methods for applet's javascript API --- src/jalview/appletgui/AlignFrame.java | 73 +- src/jalview/appletgui/AlignViewport.java | 1 + src/jalview/appletgui/FeatureRenderer.java | 1727 ++++++++++++++++------------ src/jalview/appletgui/FeatureSettings.java | 1087 +++++++++-------- src/jalview/bin/JalviewLite.java | 164 ++- 5 files changed, 1726 insertions(+), 1326 deletions(-) diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index af5a15d..85e4a1a 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -478,7 +478,7 @@ public class AlignFrame case KeyEvent.VK_T: if (evt.isControlDown()) { - newView(); + newView(null); } break; @@ -687,7 +687,7 @@ public class AlignFrame } else if (source == newView) { - newView(); + newView(null); } else if (source == showColumns) { @@ -1774,8 +1774,12 @@ public class AlignFrame { new Finder(alignPanel); } - - public void newView() + /** + * create a new view derived from the current view + * @param viewtitle + * @return frame for the new view + */ + public AlignFrame newView(String viewtitle) { AlignmentI newal; if (viewport.hasHiddenRows) @@ -1828,20 +1832,69 @@ public class AlignFrame } String title = new String(this.getTitle()); - if (title.indexOf("(View") > -1) + if (viewtitle!=null) { - title = title.substring(0, title.indexOf("(View")); + title = viewtitle+" ( "+title+")"; + } else { + if (title.indexOf("(View") > -1) + { + title = title.substring(0, title.indexOf("(View")); + } + title += "(View " + viewSize + ")"; } - title += "(View " + viewSize + ")"; - newaf.setTitle(title.toString()); newaf.viewport.historyList = viewport.historyList; newaf.viewport.redoList = viewport.redoList; - + return newaf; + } + /** + * + * @return list of feature groups on the view + */ + public String[] getFeatureGroups() + { + FeatureRenderer fr = null; + if (alignPanel!=null && (fr=alignPanel.getFeatureRenderer())!=null) + { + return fr.getGroups(); + } + return null; + } + /** + * get sequence feature groups that are hidden or shown + * @param visible true is visible + * @return list + */ + public String[] getFeatureGroupsOfState(boolean visible) + { + FeatureRenderer fr = null; + if (alignPanel!=null && (fr=alignPanel.getFeatureRenderer())!=null) + { + return fr.getGroups(visible); + } + return null; + } + /** + * Change the display state for the given feature groups + * @param groups list of group strings + * @param state visible or invisible + */ + public void setFeatureGroupState(String[] groups, boolean state) { + FeatureRenderer fr = null; + this.sequenceFeatures.setState(true); + viewport.showSequenceFeatures(true); + if (alignPanel!=null && (fr=alignPanel.getFeatureRenderer())!=null) + { + fr.setGroupState(groups, state); + alignPanel.seqPanel.seqCanvas.repaint(); + if (alignPanel.overviewPanel != null) + { + alignPanel.overviewPanel.updateOverviewImage(); + } + } } - public void seqLimits_itemStateChanged() { viewport.setShowJVSuffix(seqLimits.getState()); diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index 3418270..a4708c6 100755 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -671,6 +671,7 @@ public class AlignViewport } java.awt.Frame nullFrame; + protected FeatureSettings featureSettings=null; public void setFont(Font f) { font = f; diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index c90fb47..5e65409 100755 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -1,752 +1,975 @@ -/* - * 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 - * 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 - */ -package jalview.appletgui; - -import java.util.*; - -import java.awt.*; - -import java.awt.event.*; - - -import jalview.datamodel.*; - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class FeatureRenderer -{ - AlignViewport av; - - Hashtable featureColours = new Hashtable(); - - // A higher level for grouping features of a - // particular type - Hashtable featureGroups = null; - - // Holds web links for feature groups and feature types - // in the form label|link - Hashtable featureLinks = null; - - // This is actually an Integer held in the hashtable, - // Retrieved using the key feature type - Object currentColour; - - String[] renderOrder; - - FontMetrics fm; - int charOffset; - - float transparency = 1f; - - TransparencySetter transparencySetter = null; - - /** - * Creates a new FeatureRenderer object. - * - * @param av DOCUMENT ME! - */ - public FeatureRenderer(AlignViewport av) - { - this.av = av; - - if (!System.getProperty("java.version").startsWith("1.1")) - { - transparencySetter = new TransparencySetter(); - } - } - - public void transferSettings(FeatureRenderer fr) - { - renderOrder = fr.renderOrder; - featureGroups = fr.featureGroups; - featureColours = fr.featureColours; - transparency = fr.transparency; - } - - - static String lastFeatureAdded; - static String lastFeatureGroupAdded; - static String lastDescriptionAdded; - - int featureIndex = 0; - boolean deleteFeature = false; - Panel colourPanel; - boolean amendFeatures(final SequenceI[] sequences, - final SequenceFeature[] features, - boolean newFeatures, - final AlignmentPanel ap) - { - Panel bigPanel = new Panel(new BorderLayout()); - final TextField name = new TextField(16); - final TextField source = new TextField(16); - final TextArea description = new TextArea(3, 35); - final TextField start = new TextField(8); - final TextField end = new TextField(8); - final Choice overlaps; - Button deleteButton = new Button("Delete"); - deleteFeature = false; - - colourPanel = new Panel(null); - colourPanel.setSize(110,15); - final FeatureRenderer fr = this; - - Panel panel = new Panel(new GridLayout(3, 1)); - - Panel tmp; - - /////////////////////////////////////// - ///MULTIPLE FEATURES AT SELECTED RESIDUE - if(!newFeatures && features.length>1) - { - panel = new Panel(new GridLayout(4, 1)); - tmp = new Panel(); - tmp.add(new Label("Select Feature: ")); - overlaps = new Choice(); - for(int i=0; i0) - { - for (int i = 0; i < sequences.length; i++) - { - features[i].type = lastFeatureAdded; - features[i].featureGroup = lastFeatureGroupAdded; - features[i].description = lastDescriptionAdded; - sequences[i].addSequenceFeature(features[i]); - ffile.parseDescriptionHTML(features[i], false); - } - - if (av.featuresDisplayed == null) - { - av.featuresDisplayed = new Hashtable(); - } - - if (featureGroups == null) - { - featureGroups = new Hashtable(); - } - - col = colourPanel.getBackground(); - setColour(lastFeatureAdded, col); - - if(lastFeatureGroupAdded!=null) - { - featureGroups.put(lastFeatureGroupAdded, new Boolean(true)); - av.featuresDisplayed.put(lastFeatureGroupAdded, - new Integer(col.getRGB())); - } - findAllFeatures(); - - String [] tro = new String[renderOrder.length]; - tro[0] = renderOrder[renderOrder.length-1]; - System.arraycopy(renderOrder,0,tro,1,renderOrder.length-1); - renderOrder = tro; - - ap.paintAlignment(true); - - return true; - } - else - { - return false; - } - } - - findAllFeatures(); - - ap.paintAlignment(true); - - return true; - } - - - public Color findFeatureColour(Color initialCol, SequenceI seq, int i) - { - overview = true; - if (!av.showSequenceFeatures) - { - return initialCol; - } - - lastSeq = seq; - sequenceFeatures = lastSeq.getSequenceFeatures(); - if (sequenceFeatures == null) - { - return initialCol; - } - - sfSize = sequenceFeatures.length; - - if (jalview.util.Comparison.isGap(lastSeq.getCharAt(i))) - { - return Color.white; - } - - currentColour = null; - - drawSequence(null, lastSeq, lastSeq.findPosition(i), -1, -1); - - if (currentColour == null) - { - return initialCol; - } - - return new Color( ( (Integer) currentColour).intValue()); - } - - /** - * This is used by the Molecule Viewer to get the accurate colour - * of the rendered sequence - */ - boolean overview = false; - - - /** - * 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; - - synchronized public void drawSequence(Graphics g, SequenceI seq, - int start, int end, int y1) - { - if (seq.getSequenceFeatures() == null - || seq.getSequenceFeatures().length == 0) - { - return; - } - - if (transparencySetter != null && g != null) - { - transparencySetter.setTransparency(g, transparency); - } - - if (lastSeq == null || seq != lastSeq || sequenceFeatures!=seq.getSequenceFeatures()) - { - lastSeq = seq; - sequenceFeatures = seq.getSequenceFeatures(); - sfSize = sequenceFeatures.length; - } - - if (av.featuresDisplayed == null || renderOrder == null) - { - findAllFeatures(); - if (av.featuresDisplayed.size() < 1) - { - return; - } - - sequenceFeatures = seq.getSequenceFeatures(); - sfSize = sequenceFeatures.length; - } - if (!overview) - { - spos = lastSeq.findPosition(start); - epos = lastSeq.findPosition(end); - if (g != null) - { - fm = g.getFontMetrics(); - } - } - String type; - for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) - { - type = renderOrder[renderIndex]; - if (!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 - && - featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup) - && - ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex]. - featureGroup)). - booleanValue()) - { - continue; - } - - if (!overview && (sequenceFeatures[sfindex].getBegin() > epos - || sequenceFeatures[sfindex].getEnd() < spos)) - { - continue; - } - - if (overview) - { - if (sequenceFeatures[sfindex].begin <= start && - sequenceFeatures[sfindex].end >= start) - { - 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); - - } - else - { - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - getColour(sequenceFeatures[sfindex].type), - start, end, y1); - } - - } - } - - if (transparencySetter != null && g != null) - { - transparencySetter.setTransparency(g, 1.0f); - } - } - - 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; - } - - 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 (!av.validCharWidth) - { - continue; - } - - g.setColor(Color.white); - charOffset = (av.charWidth - fm.charWidth(s)) / 2; - g.drawString(String.valueOf(s), - charOffset + (av.charWidth * (i - start)), - (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5; - - } - } - } - - void findAllFeatures() - { - jalview.schemes.UserColourScheme ucs = new - jalview.schemes.UserColourScheme(); - - av.featuresDisplayed = new Hashtable(); - Vector allfeatures = new Vector(); - for (int i = 0; i < av.alignment.getHeight(); i++) - { - SequenceFeature[] features = av.alignment.getSequenceAt(i). - getSequenceFeatures(); - - if (features == null) - { - continue; - } - - int index = 0; - while (index < features.length) - { - if (!av.featuresDisplayed.containsKey(features[index].getType())) - { - if (getColour(features[index].getType()) == null) - { - featureColours.put(features[index].getType(), - ucs.createColourFromName(features[index]. - getType())); - } - - av.featuresDisplayed.put(features[index].getType(), - new Integer(getColour(features[index]. - getType()).getRGB())); - allfeatures.addElement(features[index].getType()); - } - index++; - } - } - - renderOrder = new String[allfeatures.size()]; - Enumeration en = allfeatures.elements(); - int i = allfeatures.size() - 1; - while (en.hasMoreElements()) - { - renderOrder[i] = en.nextElement().toString(); - i--; - } - } - - public Color getColour(String featureType) - { - if (!featureColours.containsKey(featureType)) - { - jalview.schemes.UserColourScheme ucs = new - jalview.schemes.UserColourScheme(); - Color col = ucs.createColourFromName(featureType); - featureColours.put(featureType, col); - return col; - } - else - return (Color) featureColours.get(featureType); - } - - - public void setColour(String featureType, Color col) - { - featureColours.put(featureType, col); - } - - public void setFeaturePriority(Object[][] data) - { - // 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 - if (av.featuresDisplayed != null) - { - av.featuresDisplayed.clear(); - } - - /* if (visibleNew) - { - if (av.featuresDisplayed != null) - { - av.featuresDisplayed.clear(); - } - else - { - av.featuresDisplayed = new Hashtable(); - } - } - if (data == null) - { - return; - }*/ - - - renderOrder = new String[data.length]; - - if (data.length > 0) - { - 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()) - { - av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB())); - } - - renderOrder[data.length - i - 1] = type; - } - } - } -} - -class TransparencySetter -{ - void setTransparency(Graphics g, float value) - { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite( - AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, value)); - } -} +/* + * 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 + * 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 + */ +package jalview.appletgui; + +import java.util.*; + +import java.awt.*; + +import java.awt.event.*; + + +import jalview.appletgui.FeatureSettings.MyCheckbox; +import jalview.datamodel.*; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class FeatureRenderer +{ + AlignViewport av; + + Hashtable featureColours = new Hashtable(); + + // A higher level for grouping features of a + // particular type + Hashtable featureGroups = null; + + // Holds web links for feature groups and feature types + // in the form label|link + Hashtable featureLinks = null; + + // This is actually an Integer held in the hashtable, + // Retrieved using the key feature type + Object currentColour; + + String[] renderOrder; + + FontMetrics fm; + int charOffset; + + float transparency = 1f; + + TransparencySetter transparencySetter = null; + + /** + * Creates a new FeatureRenderer object. + * + * @param av DOCUMENT ME! + */ + public FeatureRenderer(AlignViewport av) + { + this.av = av; + + if (!System.getProperty("java.version").startsWith("1.1")) + { + transparencySetter = new TransparencySetter(); + } + } + + public void transferSettings(FeatureRenderer fr) + { + renderOrder = fr.renderOrder; + featureGroups = fr.featureGroups; + featureColours = fr.featureColours; + transparency = fr.transparency; + } + + + static String lastFeatureAdded; + static String lastFeatureGroupAdded; + static String lastDescriptionAdded; + + int featureIndex = 0; + boolean deleteFeature = false; + Panel colourPanel; + boolean amendFeatures(final SequenceI[] sequences, + final SequenceFeature[] features, + boolean newFeatures, + final AlignmentPanel ap) + { + Panel bigPanel = new Panel(new BorderLayout()); + final TextField name = new TextField(16); + final TextField source = new TextField(16); + final TextArea description = new TextArea(3, 35); + final TextField start = new TextField(8); + final TextField end = new TextField(8); + final Choice overlaps; + Button deleteButton = new Button("Delete"); + deleteFeature = false; + + colourPanel = new Panel(null); + colourPanel.setSize(110,15); + final FeatureRenderer fr = this; + + Panel panel = new Panel(new GridLayout(3, 1)); + + Panel tmp; + + /////////////////////////////////////// + ///MULTIPLE FEATURES AT SELECTED RESIDUE + if(!newFeatures && features.length>1) + { + panel = new Panel(new GridLayout(4, 1)); + tmp = new Panel(); + tmp.add(new Label("Select Feature: ")); + overlaps = new Choice(); + for(int i=0; i0) + { + for (int i = 0; i < sequences.length; i++) + { + features[i].type = lastFeatureAdded; + features[i].featureGroup = lastFeatureGroupAdded; + features[i].description = lastDescriptionAdded; + sequences[i].addSequenceFeature(features[i]); + ffile.parseDescriptionHTML(features[i], false); + } + + if (av.featuresDisplayed == null) + { + av.featuresDisplayed = new Hashtable(); + } + + if (featureGroups == null) + { + featureGroups = new Hashtable(); + } + + col = colourPanel.getBackground(); + setColour(lastFeatureAdded, col); + + if(lastFeatureGroupAdded!=null) + { + featureGroups.put(lastFeatureGroupAdded, new Boolean(true)); + av.featuresDisplayed.put(lastFeatureGroupAdded, + new Integer(col.getRGB())); + } + findAllFeatures(); + + String [] tro = new String[renderOrder.length]; + tro[0] = renderOrder[renderOrder.length-1]; + System.arraycopy(renderOrder,0,tro,1,renderOrder.length-1); + renderOrder = tro; + + ap.paintAlignment(true); + + return true; + } + else + { + return false; + } + } + + findAllFeatures(); + + ap.paintAlignment(true); + + return true; + } + + + public Color findFeatureColour(Color initialCol, SequenceI seq, int i) + { + overview = true; + if (!av.showSequenceFeatures) + { + return initialCol; + } + + lastSeq = seq; + sequenceFeatures = lastSeq.getSequenceFeatures(); + if (sequenceFeatures == null) + { + return initialCol; + } + + sfSize = sequenceFeatures.length; + + if (jalview.util.Comparison.isGap(lastSeq.getCharAt(i))) + { + return Color.white; + } + + currentColour = null; + + drawSequence(null, lastSeq, lastSeq.findPosition(i), -1, -1); + + if (currentColour == null) + { + return initialCol; + } + + return new Color( ( (Integer) currentColour).intValue()); + } + + /** + * This is used by the Molecule Viewer to get the accurate colour + * of the rendered sequence + */ + boolean overview = false; + + + /** + * 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; + + synchronized public void drawSequence(Graphics g, SequenceI seq, + int start, int end, int y1) + { + if (seq.getSequenceFeatures() == null + || seq.getSequenceFeatures().length == 0) + { + return; + } + + if (transparencySetter != null && g != null) + { + transparencySetter.setTransparency(g, transparency); + } + + if (lastSeq == null || seq != lastSeq || sequenceFeatures!=seq.getSequenceFeatures()) + { + lastSeq = seq; + sequenceFeatures = seq.getSequenceFeatures(); + sfSize = sequenceFeatures.length; + } + + if (av.featuresDisplayed == null || renderOrder == null) + { + findAllFeatures(); + if (av.featuresDisplayed.size() < 1) + { + return; + } + + sequenceFeatures = seq.getSequenceFeatures(); + sfSize = sequenceFeatures.length; + } + if (!overview) + { + spos = lastSeq.findPosition(start); + epos = lastSeq.findPosition(end); + if (g != null) + { + fm = g.getFontMetrics(); + } + } + String type; + for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) + { + type = renderOrder[renderIndex]; + if (!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 + && + featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup) + && + ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex]. + featureGroup)). + booleanValue()) + { + continue; + } + + if (!overview && (sequenceFeatures[sfindex].getBegin() > epos + || sequenceFeatures[sfindex].getEnd() < spos)) + { + continue; + } + + if (overview) + { + if (sequenceFeatures[sfindex].begin <= start && + sequenceFeatures[sfindex].end >= start) + { + 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); + + } + else + { + renderFeature(g, seq, + seq.findIndex(sequenceFeatures[sfindex].begin) - 1, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, + getColour(sequenceFeatures[sfindex].type), + start, end, y1); + } + + } + } + + if (transparencySetter != null && g != null) + { + transparencySetter.setTransparency(g, 1.0f); + } + } + + 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; + } + + 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 (!av.validCharWidth) + { + continue; + } + + g.setColor(Color.white); + charOffset = (av.charWidth - fm.charWidth(s)) / 2; + g.drawString(String.valueOf(s), + charOffset + (av.charWidth * (i - start)), + (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5; + + } + } + } + + void findAllFeatures() + { + jalview.schemes.UserColourScheme ucs = new + jalview.schemes.UserColourScheme(); + + av.featuresDisplayed = new Hashtable(); + Vector allfeatures = new Vector(); + for (int i = 0; i < av.alignment.getHeight(); i++) + { + SequenceFeature[] features = av.alignment.getSequenceAt(i). + getSequenceFeatures(); + + if (features == null) + { + continue; + } + + int index = 0; + while (index < features.length) + { + if (!av.featuresDisplayed.containsKey(features[index].getType())) + { + if (getColour(features[index].getType()) == null) + { + featureColours.put(features[index].getType(), + ucs.createColourFromName(features[index]. + getType())); + } + + av.featuresDisplayed.put(features[index].getType(), + new Integer(getColour(features[index]. + getType()).getRGB())); + allfeatures.addElement(features[index].getType()); + } + index++; + } + } + + renderOrder = new String[allfeatures.size()]; + Enumeration en = allfeatures.elements(); + int i = allfeatures.size() - 1; + while (en.hasMoreElements()) + { + renderOrder[i] = en.nextElement().toString(); + i--; + } + } + + public Color getColour(String featureType) + { + if (!featureColours.containsKey(featureType)) + { + jalview.schemes.UserColourScheme ucs = new + jalview.schemes.UserColourScheme(); + Color col = ucs.createColourFromName(featureType); + featureColours.put(featureType, col); + return col; + } + else + return (Color) featureColours.get(featureType); + } + + + public void setColour(String featureType, Color col) + { + featureColours.put(featureType, col); + } + + public void setFeaturePriority(Object[][] data) + { + // 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 + if (av.featuresDisplayed != null) + { + av.featuresDisplayed.clear(); + } + + /* if (visibleNew) + { + if (av.featuresDisplayed != null) + { + av.featuresDisplayed.clear(); + } + else + { + av.featuresDisplayed = new Hashtable(); + } + } + if (data == null) + { + return; + }*/ + + + renderOrder = new String[data.length]; + + if (data.length > 0) + { + 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()) + { + av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB())); + } + + renderOrder[data.length - i - 1] = type; + } + } + } + /** + * @return a simple list of feature group names or null + */ + public String[] getGroups() + { + buildGroupHash(); + if (featureGroups!=null) + { + String[] gps = new String[featureGroups.size()]; + Enumeration gn = featureGroups.keys(); + int i=0; + while (gn.hasMoreElements()) + { + gps[i++] = (String) gn.nextElement(); + } + return gps; + } + return null; + } + /** + * get visible or invisible groups + * @param visible true to return visible groups, false to return hidden ones. + * @return list of groups + */ + public String[] getGroups(boolean visible) + { + buildGroupHash(); + if (featureGroups!=null) + { + Vector gp = new Vector(); + + Enumeration gn = featureGroups.keys(); + while (gn.hasMoreElements()) + { + String nm = (String) gn.nextElement(); + Boolean state = (Boolean) featureGroups.get(nm); + if (state.booleanValue()==visible) + { + gp.addElement(nm); + } + } + String[] gps = new String[gp.size()]; + gp.copyInto(gps); + + int i=0; + while (gn.hasMoreElements()) + { + gps[i++] = (String) gn.nextElement(); + } + return gps; + } + return null; + } + /** + * set all feature groups in toset to be visible or invisible + * @param toset group names + * @param visible the state of the named groups to set + */ + public void setGroupState(String[] toset, boolean visible) + { + buildGroupHash(); + if (toset!=null && toset.length>0 && featureGroups!=null) + { + boolean rdrw = false; + for (int i=0;i0) + { + String[] neworder = new String[allFeatures.size()]; + int p=neworder.length-1; + for (int i=renderOrder.length-1; i>=0; i--) + { + if (allFeatures.contains(renderOrder[i])) + { + neworder[p--] = renderOrder[i]; + allFeatures.removeElement(renderOrder[i]); + } else { + av.featuresDisplayed.remove(renderOrder[i]); + } + } + for (int i=allFeatures.size()-1; i>0; i++) + { + Object e = allFeatures.elementAt(i); + if (e!=null) + { + neworder[p--] = (String) e; + av.featuresDisplayed.put(e, getColour((String)e)); + } + } + renderOrder = neworder; + return true; + } + + return alignmentHasFeatures; + } +} + +class TransparencySetter +{ + void setTransparency(Graphics g, float value) + { + Graphics2D g2 = (Graphics2D) g; + g2.setComposite( + AlphaComposite.getInstance( + AlphaComposite.SRC_OVER, value)); + } +} diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java index 7dc11c1..f2e44f5 100755 --- a/src/jalview/appletgui/FeatureSettings.java +++ b/src/jalview/appletgui/FeatureSettings.java @@ -1,547 +1,540 @@ -/* - * 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 - * 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 - */ -package jalview.appletgui; - -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.datamodel.*; - -public class FeatureSettings - extends Panel implements ItemListener, - MouseListener, MouseMotionListener, ActionListener, AdjustmentListener -{ - FeatureRenderer fr; - AlignmentPanel ap; - AlignViewport av; - Frame frame; - Panel groupPanel; - Panel featurePanel = new Panel(); - ScrollPane scrollPane; - boolean alignmentHasFeatures = false; - Image linkImage; - Scrollbar transparency; - - public FeatureSettings(final AlignmentPanel ap) - { - this.ap = ap; - this.av = ap.av; - fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); - - transparency = new Scrollbar(Scrollbar.HORIZONTAL, - 100 - (int) (fr.transparency * 100), 1, 1, 100); - - if (fr.transparencySetter != null) - { - transparency.addAdjustmentListener(this); - } - else - { - transparency.setEnabled(false); - } - - java.net.URL url = getClass().getResource("/images/link.gif"); - if (url != null) - { - linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url); - } - - if (av.featuresDisplayed == null) - { - fr.findAllFeatures(); - } - - setTableData(); - - this.setLayout(new BorderLayout()); - scrollPane = new ScrollPane(); - scrollPane.add(featurePanel); - if (alignmentHasFeatures) - { - add(scrollPane, BorderLayout.CENTER); - } - - Button invert = new Button("Invert Selection"); - invert.addActionListener(this); - - Panel lowerPanel = new Panel(new GridLayout(2, 1, 5, 10)); - lowerPanel.add(invert); - - Panel tPanel = new Panel(new BorderLayout()); - - if (fr.transparencySetter != null) - { - tPanel.add(transparency, BorderLayout.CENTER); - tPanel.add(new Label("Transparency"), BorderLayout.EAST); - } - else - { - tPanel.add(new Label("Transparency not available in this web browser"), - BorderLayout.CENTER); - } - - lowerPanel.add(tPanel, BorderLayout.SOUTH); - - add(lowerPanel, BorderLayout.SOUTH); - - if (groupPanel != null) - { - groupPanel.setLayout( - new GridLayout(fr.featureGroups.size() / 4 + 1, 4)); - groupPanel.validate(); - - add(groupPanel, BorderLayout.NORTH); - } - frame = new Frame(); - frame.add(this); - int height = featurePanel.getComponentCount() * 50 + 60; - - height = Math.max(200, height); - height = Math.min(400, height); - - jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", 280, - height); - } - - public void paint(Graphics g) - { - g.setColor(Color.black); - g.drawString("No Features added to this alignment!!", 10, 20); - g.drawString("(Features can be added from searches or", 10, 40); - g.drawString("from Jalview / GFF features files)", 10, 60); - } - - void setTableData() - { - alignmentHasFeatures = false; - - if (fr.featureGroups == null) - { - fr.featureGroups = new Hashtable(); - } - - Vector allFeatures = new Vector(); - Vector allGroups = new Vector(); - SequenceFeature[] tmpfeatures; - String group; - - for (int i = 0; i < av.alignment.getHeight(); i++) - { - if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null) - { - continue; - } - - alignmentHasFeatures = true; - - tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures(); - int index = 0; - while (index < tmpfeatures.length) - { - if (tmpfeatures[index].getFeatureGroup() != null) - { - group = tmpfeatures[index].featureGroup; - if (!allGroups.contains(group)) - { - allGroups.addElement(group); - - boolean visible = true; - if (fr.featureGroups.containsKey(group)) - { - visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue(); - } - - fr.featureGroups.put(group, new Boolean(visible)); - - if (groupPanel == null) - { - groupPanel = new Panel(); - } - - Checkbox check = new MyCheckbox( - group, - visible, - (fr.featureLinks != null && fr.featureLinks.containsKey(group)) - ); - - check.addMouseListener(this); - check.setFont(new Font("Serif", Font.BOLD, 12)); - check.addItemListener(this); - groupPanel.add(check); - } - } - - if (!allFeatures.contains(tmpfeatures[index].getType())) - { - allFeatures.addElement(tmpfeatures[index].getType()); - } - index++; - } - } - - resetTable(false); - } - - //This routine adds and removes checkboxes depending on - //Group selection states - void resetTable(boolean groupsChanged) - { - SequenceFeature[] tmpfeatures; - String group = null, type; - Vector visibleChecks = new Vector(); - - for (int i = 0; i < av.alignment.getHeight(); i++) - { - if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null) - { - continue; - } - - tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures(); - int index = 0; - while (index < tmpfeatures.length) - { - group = tmpfeatures[index].featureGroup; - - if (group == null || fr.featureGroups.get(group) == null || - ( (Boolean) fr.featureGroups.get(group)).booleanValue()) - { - type = tmpfeatures[index].getType(); - if (!visibleChecks.contains(type)) - { - visibleChecks.addElement(type); - } - } - index++; - } - } - - Component[] comps; - int cSize = featurePanel.getComponentCount(); - Checkbox check; - //This will remove any checkboxes which shouldn't be - //visible - for (int i = 0; i < cSize; i++) - { - comps = featurePanel.getComponents(); - check = (Checkbox) comps[i]; - if (!visibleChecks.contains(check.getLabel())) - { - featurePanel.remove(i); - cSize--; - i--; - } - } - - if (fr.renderOrder != null) - { - //First add the checks in the previous render order, - //in case the window has been closed and reopened - for (int ro = fr.renderOrder.length - 1; ro > -1; ro--) - { - String item = fr.renderOrder[ro]; - - if (!visibleChecks.contains(item)) - { - continue; - } - - visibleChecks.removeElement(item); - - addCheck(false, item); - } - } - - // now add checkboxes which should be visible, - // if they have not already been added - Enumeration en = visibleChecks.elements(); - - while (en.hasMoreElements()) - { - addCheck(groupsChanged, en.nextElement().toString()); - } - - featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(), 1, - 10, 5)); - featurePanel.validate(); - - if (scrollPane != null) - { - scrollPane.validate(); - } - - itemStateChanged(null); - } - - void addCheck(boolean groupsChanged, String type) - { - boolean addCheck; - Component[] comps = featurePanel.getComponents(); - Checkbox check; - addCheck = true; - for (int i = 0; i < featurePanel.getComponentCount(); i++) - { - check = (Checkbox) comps[i]; - if (check.getLabel().equals(type)) - { - addCheck = false; - break; - } - } - - if (addCheck) - { - boolean selected = false; - if (groupsChanged || av.featuresDisplayed.containsKey(type)) - { - selected = true; - } - - check = new MyCheckbox(type, - selected, - (fr.featureLinks != null && - fr.featureLinks.containsKey(type)) - ); - - check.addMouseListener(this); - check.addMouseMotionListener(this); - check.setBackground(fr.getColour(type)); - check.addItemListener(this); - featurePanel.add(check); - } - } - - public void actionPerformed(ActionEvent evt) - { - for (int i = 0; i < featurePanel.getComponentCount(); i++) - { - Checkbox check = (Checkbox) featurePanel.getComponent(i); - check.setState(!check.getState()); - } - selectionChanged(); - } - - public void itemStateChanged(ItemEvent evt) - { - if (evt != null) - { - //Is the source a top level featureGroup? - Checkbox source = (Checkbox) evt.getSource(); - if (fr.featureGroups.containsKey(source.getLabel())) - { - fr.featureGroups.put(source.getLabel(), new Boolean(source.getState())); - ap.seqPanel.seqCanvas.repaint(); - if (ap.overviewPanel != null) - { - ap.overviewPanel.updateOverviewImage(); - } - - resetTable(true); - return; - } - } - selectionChanged(); - } - - void selectionChanged() - { - Component[] comps = featurePanel.getComponents(); - int cSize = comps.length; - - Object[][] tmp = new Object[cSize][3]; - int tmpSize = 0; - for (int i = 0; i < cSize; i++) - { - Checkbox check = (Checkbox) comps[i]; - tmp[tmpSize][0] = check.getLabel(); - tmp[tmpSize][1] = fr.getColour(check.getLabel()); - tmp[tmpSize][2] = new Boolean(check.getState()); - tmpSize++; - } - - Object[][] data = new Object[tmpSize][3]; - System.arraycopy(tmp, 0, data, 0, tmpSize); - - fr.setFeaturePriority(data); - - ap.paintAlignment(true); - } - - MyCheckbox selectedCheck; - boolean dragging = false; - - public void mousePressed(MouseEvent evt) - { - - selectedCheck = (MyCheckbox) evt.getSource(); - - if (fr.featureLinks != null - && fr.featureLinks.containsKey(selectedCheck.getLabel()) - ) - { - if (evt.getX() > selectedCheck.stringWidth + 20) - { - evt.consume(); - } - } - - } - - public void mouseDragged(MouseEvent evt) - { - if ( ( (Component) evt.getSource()).getParent() != featurePanel) - { - return; - } - dragging = true; - } - - public void mouseReleased(MouseEvent evt) - { - if ( ( (Component) evt.getSource()).getParent() != featurePanel) - { - return; - } - - Component comp = null; - Checkbox target = null; - - int height = evt.getY() + evt.getComponent().getLocation().y; - - if (height > featurePanel.getSize().height) - { - - comp = featurePanel.getComponent(featurePanel.getComponentCount() - 1); - } - else if (height < 0) - { - comp = featurePanel.getComponent(0); - } - else - { - comp = featurePanel.getComponentAt(evt.getX(), - evt.getY() + - evt.getComponent().getLocation().y); - } - - if (comp != null && comp instanceof Checkbox) - { - target = (Checkbox) comp; - } - - if (selectedCheck != null - && target != null - && selectedCheck != target) - { - int targetIndex = -1; - for (int i = 0; i < featurePanel.getComponentCount(); i++) - { - if (target == featurePanel.getComponent(i)) - { - targetIndex = i; - break; - } - } - - featurePanel.remove(selectedCheck); - featurePanel.add(selectedCheck, targetIndex); - featurePanel.validate(); - itemStateChanged(null); - } - } - - public void setUserColour(String feature, Color col) - { - fr.setColour(feature, col); - featurePanel.removeAll(); - resetTable(false); - ap.paintAlignment(true); - } - - public void mouseEntered(MouseEvent evt) - {} - - public void mouseExited(MouseEvent evt) - {} - - public void mouseClicked(MouseEvent evt) - { - MyCheckbox check = (MyCheckbox) evt.getSource(); - - if (fr.featureLinks != null - && fr.featureLinks.containsKey(check.getLabel())) - { - if (evt.getX() > check.stringWidth + 20) - { - evt.consume(); - String link = fr.featureLinks.get(check.getLabel()).toString(); - ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1), - link.substring(0, link.indexOf("|"))); - } - } - - if (check.getParent() != featurePanel) - { - return; - } - - if (evt.getClickCount() > 1) - { - new UserDefinedColours(this, check.getLabel(), - fr.getColour(check.getLabel())); - } - } - - public void mouseMoved(MouseEvent evt) - {} - - public void adjustmentValueChanged(AdjustmentEvent evt) - { - fr.transparency = ( (float) (100 - transparency.getValue()) / 100f); - ap.seqPanel.seqCanvas.repaint(); - - } - - class MyCheckbox - extends Checkbox - { - public int stringWidth; - boolean hasLink; - public MyCheckbox(String label, boolean checked, boolean haslink) - { - super(label, checked); - - FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont()); - stringWidth = fm.stringWidth(label); - this.hasLink = haslink; - } - - public void paint(Graphics g) - { - if (hasLink) - { - g.drawImage(linkImage, stringWidth + 25, ( - getSize().height - linkImage.getHeight(this)) / 2, - this); - } - } - } -} +/* + * 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 + * 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 + */ +package jalview.appletgui; + +import java.util.*; + +import java.awt.*; +import java.awt.event.*; + +import jalview.datamodel.*; + +public class FeatureSettings + extends Panel implements ItemListener, + MouseListener, MouseMotionListener, ActionListener, AdjustmentListener +{ + FeatureRenderer fr; + AlignmentPanel ap; + AlignViewport av; + Frame frame; + Panel groupPanel; + Panel featurePanel = new Panel(); + ScrollPane scrollPane; + boolean alignmentHasFeatures = false; + Image linkImage; + Scrollbar transparency; + + public FeatureSettings(final AlignmentPanel ap) + { + this.ap = ap; + this.av = ap.av; + ap.av.featureSettings = this; + fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); + + transparency = new Scrollbar(Scrollbar.HORIZONTAL, + 100 - (int) (fr.transparency * 100), 1, 1, 100); + + if (fr.transparencySetter != null) + { + transparency.addAdjustmentListener(this); + } + else + { + transparency.setEnabled(false); + } + + java.net.URL url = getClass().getResource("/images/link.gif"); + if (url != null) + { + linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url); + } + + if (av.featuresDisplayed == null) + { + fr.findAllFeatures(); + } + + setTableData(); + + this.setLayout(new BorderLayout()); + scrollPane = new ScrollPane(); + scrollPane.add(featurePanel); + if (alignmentHasFeatures) + { + add(scrollPane, BorderLayout.CENTER); + } + + Button invert = new Button("Invert Selection"); + invert.addActionListener(this); + + Panel lowerPanel = new Panel(new GridLayout(2, 1, 5, 10)); + lowerPanel.add(invert); + + Panel tPanel = new Panel(new BorderLayout()); + + if (fr.transparencySetter != null) + { + tPanel.add(transparency, BorderLayout.CENTER); + tPanel.add(new Label("Transparency"), BorderLayout.EAST); + } + else + { + tPanel.add(new Label("Transparency not available in this web browser"), + BorderLayout.CENTER); + } + + lowerPanel.add(tPanel, BorderLayout.SOUTH); + + add(lowerPanel, BorderLayout.SOUTH); + + if (groupPanel != null) + { + groupPanel.setLayout( + new GridLayout(fr.featureGroups.size() / 4 + 1, 4)); + groupPanel.validate(); + + add(groupPanel, BorderLayout.NORTH); + } + frame = new Frame(); + frame.add(this); + final FeatureSettings me = this; + frame.addWindowListener(new WindowAdapter() + { + public void windowClosing(WindowEvent e) + { + if (me.av.featureSettings==me) + { + me.av.featureSettings = null; + me.ap = null; + me.av = null; + } + } + } + ); + int height = featurePanel.getComponentCount() * 50 + 60; + + height = Math.max(200, height); + height = Math.min(400, height); + int width = 300; + jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", width, + height); + } + + public void paint(Graphics g) + { + g.setColor(Color.black); + g.drawString("No Features added to this alignment!!", 10, 20); + g.drawString("(Features can be added from searches or", 10, 40); + g.drawString("from Jalview / GFF features files)", 10, 60); + } + + public void setTableData() + { + alignmentHasFeatures = fr.buildGroupHash(); + if (alignmentHasFeatures) + { + rebuildGroups(); + + } + resetTable(false); + } + /** + * rebuilds the group panel + */ + public void rebuildGroups() + { + boolean rdrw = false; + if (groupPanel == null) + { + groupPanel = new Panel(); + } else { + rdrw = true; + groupPanel.removeAll(); + } + + Enumeration gps = fr.featureGroups.keys(); + while (gps.hasMoreElements()) + { + String group = (String) gps.nextElement(); + Boolean vis = (Boolean) fr.featureGroups.get(group); + Checkbox check = new MyCheckbox( + group, + vis.booleanValue(), + (fr.featureLinks != null && fr.featureLinks.containsKey(group)) + ); + check.addMouseListener(this); + check.setFont(new Font("Serif", Font.BOLD, 12)); + check.addItemListener(this); + groupPanel.add(check); + } + if (rdrw) + { + groupPanel.validate(); + } + } + + //This routine adds and removes checkboxes depending on + //Group selection states + void resetTable(boolean groupsChanged) + { + SequenceFeature[] tmpfeatures; + String group = null, type; + Vector visibleChecks = new Vector(); + + for (int i = 0; i < av.alignment.getHeight(); i++) + { + if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null) + { + continue; + } + + tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures(); + int index = 0; + while (index < tmpfeatures.length) + { + group = tmpfeatures[index].featureGroup; + + if (group == null || fr.featureGroups.get(group) == null || + ( (Boolean) fr.featureGroups.get(group)).booleanValue()) + { + type = tmpfeatures[index].getType(); + if (!visibleChecks.contains(type)) + { + visibleChecks.addElement(type); + } + } + index++; + } + } + + Component[] comps; + int cSize = featurePanel.getComponentCount(); + Checkbox check; + //This will remove any checkboxes which shouldn't be + //visible + for (int i = 0; i < cSize; i++) + { + comps = featurePanel.getComponents(); + check = (Checkbox) comps[i]; + if (!visibleChecks.contains(check.getLabel())) + { + featurePanel.remove(i); + cSize--; + i--; + } + } + + if (fr.renderOrder != null) + { + //First add the checks in the previous render order, + //in case the window has been closed and reopened + for (int ro = fr.renderOrder.length - 1; ro > -1; ro--) + { + String item = fr.renderOrder[ro]; + + if (!visibleChecks.contains(item)) + { + continue; + } + + visibleChecks.removeElement(item); + + addCheck(false, item); + } + } + + // now add checkboxes which should be visible, + // if they have not already been added + Enumeration en = visibleChecks.elements(); + + while (en.hasMoreElements()) + { + addCheck(groupsChanged, en.nextElement().toString()); + } + + featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(), 1, + 10, 5)); + featurePanel.validate(); + + if (scrollPane != null) + { + scrollPane.validate(); + } + + itemStateChanged(null); + } + /** + * update the checklist of feature types with the given type + * @param groupsChanged true means if the type is not in the display list then it will be added and displayed + * @param type feature type to be checked for in the list. + */ + void addCheck(boolean groupsChanged, String type) + { + boolean addCheck; + Component[] comps = featurePanel.getComponents(); + Checkbox check; + addCheck = true; + for (int i = 0; i < featurePanel.getComponentCount(); i++) + { + check = (Checkbox) comps[i]; + if (check.getLabel().equals(type)) + { + addCheck = false; + break; + } + } + + if (addCheck) + { + boolean selected = false; + if (groupsChanged || av.featuresDisplayed.containsKey(type)) + { + selected = true; + } + + check = new MyCheckbox(type, + selected, + (fr.featureLinks != null && + fr.featureLinks.containsKey(type)) + ); + + check.addMouseListener(this); + check.addMouseMotionListener(this); + check.setBackground(fr.getColour(type)); + check.addItemListener(this); + featurePanel.add(check); + } + } + + public void actionPerformed(ActionEvent evt) + { + for (int i = 0; i < featurePanel.getComponentCount(); i++) + { + Checkbox check = (Checkbox) featurePanel.getComponent(i); + check.setState(!check.getState()); + } + selectionChanged(); + } + + public void itemStateChanged(ItemEvent evt) + { + if (evt != null) + { + //Is the source a top level featureGroup? + Checkbox source = (Checkbox) evt.getSource(); + if (fr.featureGroups.containsKey(source.getLabel())) + { + fr.featureGroups.put(source.getLabel(), new Boolean(source.getState())); + ap.seqPanel.seqCanvas.repaint(); + if (ap.overviewPanel != null) + { + ap.overviewPanel.updateOverviewImage(); + } + + resetTable(true); + return; + } + } + selectionChanged(); + } + + void selectionChanged() + { + Component[] comps = featurePanel.getComponents(); + int cSize = comps.length; + + Object[][] tmp = new Object[cSize][3]; + int tmpSize = 0; + for (int i = 0; i < cSize; i++) + { + Checkbox check = (Checkbox) comps[i]; + tmp[tmpSize][0] = check.getLabel(); + tmp[tmpSize][1] = fr.getColour(check.getLabel()); + tmp[tmpSize][2] = new Boolean(check.getState()); + tmpSize++; + } + + Object[][] data = new Object[tmpSize][3]; + System.arraycopy(tmp, 0, data, 0, tmpSize); + + fr.setFeaturePriority(data); + + ap.paintAlignment(true); + } + + MyCheckbox selectedCheck; + boolean dragging = false; + + public void mousePressed(MouseEvent evt) + { + + selectedCheck = (MyCheckbox) evt.getSource(); + + if (fr.featureLinks != null + && fr.featureLinks.containsKey(selectedCheck.getLabel()) + ) + { + if (evt.getX() > selectedCheck.stringWidth + 20) + { + evt.consume(); + } + } + + } + + public void mouseDragged(MouseEvent evt) + { + if ( ( (Component) evt.getSource()).getParent() != featurePanel) + { + return; + } + dragging = true; + } + + public void mouseReleased(MouseEvent evt) + { + if ( ( (Component) evt.getSource()).getParent() != featurePanel) + { + return; + } + + Component comp = null; + Checkbox target = null; + + int height = evt.getY() + evt.getComponent().getLocation().y; + + if (height > featurePanel.getSize().height) + { + + comp = featurePanel.getComponent(featurePanel.getComponentCount() - 1); + } + else if (height < 0) + { + comp = featurePanel.getComponent(0); + } + else + { + comp = featurePanel.getComponentAt(evt.getX(), + evt.getY() + + evt.getComponent().getLocation().y); + } + + if (comp != null && comp instanceof Checkbox) + { + target = (Checkbox) comp; + } + + if (selectedCheck != null + && target != null + && selectedCheck != target) + { + int targetIndex = -1; + for (int i = 0; i < featurePanel.getComponentCount(); i++) + { + if (target == featurePanel.getComponent(i)) + { + targetIndex = i; + break; + } + } + + featurePanel.remove(selectedCheck); + featurePanel.add(selectedCheck, targetIndex); + featurePanel.validate(); + itemStateChanged(null); + } + } + + public void setUserColour(String feature, Color col) + { + fr.setColour(feature, col); + featurePanel.removeAll(); + resetTable(false); + ap.paintAlignment(true); + } + + public void mouseEntered(MouseEvent evt) + {} + + public void mouseExited(MouseEvent evt) + {} + + public void mouseClicked(MouseEvent evt) + { + MyCheckbox check = (MyCheckbox) evt.getSource(); + + if (fr.featureLinks != null + && fr.featureLinks.containsKey(check.getLabel())) + { + if (evt.getX() > check.stringWidth + 20) + { + evt.consume(); + String link = fr.featureLinks.get(check.getLabel()).toString(); + ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1), + link.substring(0, link.indexOf("|"))); + } + } + + if (check.getParent() != featurePanel) + { + return; + } + + if (evt.getClickCount() > 1) + { + new UserDefinedColours(this, check.getLabel(), + fr.getColour(check.getLabel())); + } + } + + public void mouseMoved(MouseEvent evt) + {} + + public void adjustmentValueChanged(AdjustmentEvent evt) + { + fr.transparency = ( (float) (100 - transparency.getValue()) / 100f); + ap.seqPanel.seqCanvas.repaint(); + + } + + class MyCheckbox + extends Checkbox + { + public int stringWidth; + boolean hasLink; + public MyCheckbox(String label, boolean checked, boolean haslink) + { + super(label, checked); + + FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont()); + stringWidth = fm.stringWidth(label); + this.hasLink = haslink; + } + + public void paint(Graphics g) + { + if (hasLink) + { + g.drawImage(linkImage, stringWidth + 25, ( + getSize().height - linkImage.getHeight(this)) / 2, + this); + } + } + } +} diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index df11327..4d1c216 100755 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -43,16 +43,22 @@ public class JalviewLite /////////////////////////////////////////// //The following public methods maybe called //externally, eg via javascript in HTML page - + /** + * @return list of selected sequences separated by "¬" + */ public String getSelectedSequences() { + return getSelectedSequences(currentAlignFrame); + } + public String getSelectedSequences(AlignFrame alf) + { StringBuffer result = new StringBuffer(""); - if (initialAlignFrame.viewport.getSelectionGroup() != null) + if (alf.viewport.getSelectionGroup() != null) { - SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup(). + SequenceI[] seqs = alf.viewport.getSelectionGroup(). getSequencesInOrder( - initialAlignFrame.viewport.getAlignment()); + alf.viewport.getAlignment()); for (int i = 0; i < seqs.length; i++) { @@ -62,20 +68,27 @@ public class JalviewLite return result.toString(); } - + public String getAlignment(String format) { - return getAlignment(format, "true"); + return getAlignment(currentAlignFrame, format, "true"); + } + public String getAlignment(AlignFrame alf, String format) + { + return getAlignment(alf, format, "true"); } - public String getAlignment(String format, String suffix) { + return getAlignment(currentAlignFrame, format, suffix); + } + public String getAlignment(AlignFrame alf, String format, String suffix) + { try { boolean seqlimits = suffix.equalsIgnoreCase("true"); String reply = new AppletFormatAdapter().formatSequences(format, - currentAlignFrame.viewport.getAlignment(), seqlimits); + alf.viewport.getAlignment(), seqlimits); return reply; } catch (Exception ex) @@ -87,30 +100,63 @@ public class JalviewLite public void loadAnnotation(String annotation) { + loadAnnotation(currentAlignFrame, annotation); + } + public void loadAnnotation(AlignFrame alf, String annotation) + { if (new AnnotationFile().readAnnotationFile( - currentAlignFrame.getAlignViewport().getAlignment(), annotation, + alf.getAlignViewport().getAlignment(), annotation, AppletFormatAdapter.PASTE)) { - currentAlignFrame.alignPanel.fontChanged(); - currentAlignFrame.alignPanel.setScrollValues(0, 0); + alf.alignPanel.fontChanged(); + alf.alignPanel.setScrollValues(0, 0); } else { - currentAlignFrame.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE); + alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE); } } public String getFeatures(String format) { - return currentAlignFrame.outputFeatures(false, format); + return getFeatures(currentAlignFrame, format); + } + public String getFeatures(AlignFrame alf, String format) + { + return alf.outputFeatures(false, format); } - public String getAnnotation() { - return currentAlignFrame.outputAnnotations(false); + return getAnnotation(currentAlignFrame); + } + public String getAnnotation(AlignFrame alf) + { + return alf.outputAnnotations(false); + } + public AlignFrame newView() + { + return newView(currentAlignFrame); + } + public AlignFrame newView(String name) + { + return newView(currentAlignFrame, name); } - public void loadAlignment(String text, String title) + public AlignFrame newView(AlignFrame alf) + { + return alf.newView(null); + } + public AlignFrame newView(AlignFrame alf, String name) + { + return alf.newView(name); + } + /** + * + * @param text alignment file as a string + * @param title window title + * @return null or new alignment frame + */ + public AlignFrame loadAlignment(String text, String title) { Alignment al = null; String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE); @@ -121,13 +167,14 @@ public class JalviewLite format); if (al.getHeight() > 0) { - new AlignFrame(al, this, title, false); + return new AlignFrame(al, this, title, false); } } catch (java.io.IOException ex) { ex.printStackTrace(); } + return null; } //////////////////////////////////////////////// @@ -276,6 +323,7 @@ public class JalviewLite if (frame instanceof AlignFrame) { currentAlignFrame = (AlignFrame) frame; + System.err.println("Activated window "+frame); } } @@ -643,4 +691,86 @@ public class JalviewLite return file; } } + + public String[] tabbedListToArray(String list) + { + if (list==null || list.equals("")) + return null; + java.util.Vector jv = new Vector(); + int cp=0,pos; + while ((pos=list.indexOf("\t",cp))>cp) + { + jv.addElement(list.substring(cp,pos)); + cp = pos+1; + } + if (cp0) + { String[] v = new String[jv.size()]; + jv.copyInto(v); + jv.removeAllElements(); + System.err.println("Array from Tabbed List:\n"+v.length+"\n"+v.toString()); + return v; + } + System.err.println("Empty Array from Tabbed List"); + return null; + } + + public String ArraytotabbedList(String[] list) + { + StringBuffer v = new StringBuffer(); + if (list!=null) + { + for (int i=0,iSize=list.length-1;i