X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=db7d9b368bb7c8b06a895d7652d5d69aa27932cc;hb=f6b39bebb91c2b69c1e5c572e7aa116e5ab19864;hp=4649786f1c363ff5c37f6b6736824885ac20a662;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java index 4649786..db7d9b3 100755 --- a/src/jalview/appletgui/FeatureSettings.java +++ b/src/jalview/appletgui/FeatureSettings.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.appletgui; @@ -23,7 +22,11 @@ import java.util.*; import java.awt.*; import java.awt.event.*; +import jalview.analysis.AlignmentSorter; +import jalview.commands.OrderCommand; import jalview.datamodel.*; +import jalview.schemes.AnnotationColourGradient; +import jalview.schemes.GraduatedColor; public class FeatureSettings extends Panel implements ItemListener, MouseListener, MouseMotionListener, ActionListener, @@ -115,8 +118,10 @@ public class FeatureSettings extends Panel implements ItemListener, if (groupPanel != null) { - groupPanel.setLayout(new GridLayout(fr.featureGroups.size() / 4 + 1, - 4)); + groupPanel + .setLayout(new GridLayout( + (fr.featureGroups.size() - fr.hiddenGroups.size()) / 4 + 1, + 4)); groupPanel.validate(); add(groupPanel, BorderLayout.NORTH); @@ -153,6 +158,85 @@ public class FeatureSettings extends Panel implements ItemListener, g.drawString("from Jalview / GFF features files)", 10, 60); } + protected void popupSort(final MyCheckbox check, final Hashtable minmax, + int x, int y) + { + final String type = check.type; + final Object typeCol = fr.getFeatureStyle(type); + java.awt.PopupMenu men = new PopupMenu("Settings for " + type); + java.awt.MenuItem scr = new MenuItem("Sort by Score"); + men.add(scr); + final FeatureSettings me = this; + scr.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + me.sortByScore(new String[] + { type }); + } + + }); + MenuItem dens = new MenuItem("Sort by Density"); + dens.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + me.sortByDens(new String[] + { type }); + } + + }); + men.add(dens); + if (minmax != null) + { + final Object typeMinMax = minmax.get(type); + /* + * final java.awt.CheckboxMenuItem chb = new + * java.awt.CheckboxMenuItem("Vary Height"); // this is broken at the + * moment chb.setState(minmax.get(type) != null); + * chb.addActionListener(new ActionListener() { + * + * public void actionPerformed(ActionEvent e) { + * chb.setState(chb.getState()); if (chb.getState()) { minmax.put(type, + * null); } else { minmax.put(type, typeMinMax); } } + * + * }); men.add(chb); + */ + if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null) + { + // graduated colourschemes for those where minmax exists for the + // positional features + MenuItem mxcol = new MenuItem( + (typeCol instanceof Color) ? "Graduated Colour" + : "Single Colour"); + men.add(mxcol); + mxcol.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + if (typeCol instanceof Color) + { + new FeatureColourChooser(me, type); + // write back the current colour object to update the table + check.updateColor(fr.getFeatureStyle(type)); + } + else + { + new UserDefinedColours(me, check.type, + ((GraduatedColor) typeCol)); + } + } + + }); + } + } + this.featurePanel.add(men); + men.show(this.featurePanel, x, y); + } + public void setTableData() { alignmentHasFeatures = fr.buildGroupHash(); @@ -179,7 +263,8 @@ public class FeatureSettings extends Panel implements ItemListener, rdrw = true; groupPanel.removeAll(); } - + // TODO: JAL-964 - smoothly incorporate new group entries if panel already + // displayed and new groups present Enumeration gps = fr.featureGroups.keys(); while (gps.hasMoreElements()) { @@ -191,6 +276,7 @@ public class FeatureSettings extends Panel implements ItemListener, check.addMouseListener(this); check.setFont(new Font("Serif", Font.BOLD, 12)); check.addItemListener(this); + check.setVisible(fr.hiddenGroups.contains(group)); groupPanel.add(check); } if (rdrw) @@ -206,15 +292,15 @@ public class FeatureSettings extends Panel implements ItemListener, SequenceFeature[] tmpfeatures; String group = null, type; Vector visibleChecks = new Vector(); - - for (int i = 0; i < av.alignment.getHeight(); i++) + AlignmentI alignment = av.getAlignment(); + for (int i = 0; i < alignment.getHeight(); i++) { - if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null) + if (alignment.getSequenceAt(i).getSequenceFeatures() == null) { continue; } - tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures(); + tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures(); int index = 0; while (index < tmpfeatures.length) { @@ -235,14 +321,14 @@ public class FeatureSettings extends Panel implements ItemListener, Component[] comps; int cSize = featurePanel.getComponentCount(); - Checkbox check; + MyCheckbox 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())) + check = (MyCheckbox) comps[i]; + if (!visibleChecks.contains(check.type)) { featurePanel.remove(i); cSize--; @@ -294,21 +380,21 @@ public class FeatureSettings extends Panel implements ItemListener, * 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 + * 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. + * feature type to be checked for in the list. */ void addCheck(boolean groupsChanged, String type) { boolean addCheck; Component[] comps = featurePanel.getComponents(); - Checkbox check; + MyCheckbox check; addCheck = true; for (int i = 0; i < featurePanel.getComponentCount(); i++) { - check = (Checkbox) comps[i]; - if (check.getLabel().equals(type)) + check = (MyCheckbox) comps[i]; + if (check.type.equals(type)) { addCheck = false; break; @@ -326,11 +412,11 @@ public class FeatureSettings extends Panel implements ItemListener, check = new MyCheckbox( type, selected, - (fr.featureLinks != null && fr.featureLinks.containsKey(type))); + (fr.featureLinks != null && fr.featureLinks.containsKey(type)), + fr.getFeatureStyle(type)); check.addMouseListener(this); check.addMouseMotionListener(this); - check.setBackground(fr.getColour(type)); check.addItemListener(this); if (groupsChanged) { @@ -363,8 +449,8 @@ public class FeatureSettings extends Panel implements ItemListener, Checkbox source = (Checkbox) evt.getSource(); if (fr.featureGroups.containsKey(source.getLabel())) { - fr.featureGroups.put(source.getLabel(), new Boolean(source - .getState())); + fr.featureGroups.put(source.getLabel(), + new Boolean(source.getState())); ap.seqPanel.seqCanvas.repaint(); if (ap.overviewPanel != null) { @@ -387,9 +473,9 @@ public class FeatureSettings extends Panel implements ItemListener, 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()); + MyCheckbox check = (MyCheckbox) comps[i]; + tmp[tmpSize][0] = check.type; + tmp[tmpSize][1] = fr.getFeatureStyle(check.type); tmp[tmpSize][2] = new Boolean(check.getState()); tmpSize++; } @@ -412,7 +498,7 @@ public class FeatureSettings extends Panel implements ItemListener, selectedCheck = (MyCheckbox) evt.getSource(); if (fr.featureLinks != null - && fr.featureLinks.containsKey(selectedCheck.getLabel())) + && fr.featureLinks.containsKey(selectedCheck.type)) { if (evt.getX() > selectedCheck.stringWidth + 20) { @@ -483,9 +569,23 @@ public class FeatureSettings extends Panel implements ItemListener, } } - public void setUserColour(String feature, Color col) + public void setUserColour(String feature, Object originalColour) + { + if (originalColour instanceof Color + || originalColour instanceof GraduatedColor) + { + fr.setColour(feature, originalColour); + } + else + { + throw new Error( + "Implementation error: Unsupported feature colour object."); + } + refreshTable(); + } + + public void refreshTable() { - fr.setColour(feature, col); featurePanel.removeAll(); resetTable(false); ap.paintAlignment(true); @@ -502,16 +602,18 @@ public class FeatureSettings extends Panel implements ItemListener, public void mouseClicked(MouseEvent evt) { MyCheckbox check = (MyCheckbox) evt.getSource(); - - if (fr.featureLinks != null - && fr.featureLinks.containsKey(check.getLabel())) + if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0) + { + this.popupSort(check, fr.minmax, evt.getX(), evt.getY()); + } + if (fr.featureLinks != null && fr.featureLinks.containsKey(check.type)) { 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("|"))); + String link = fr.featureLinks.get(check.type).toString(); + ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1), + link.substring(0, link.indexOf("|"))); } } @@ -522,8 +624,17 @@ public class FeatureSettings extends Panel implements ItemListener, if (evt.getClickCount() > 1) { - new UserDefinedColours(this, check.getLabel(), fr.getColour(check - .getLabel())); + Object fcol = fr.getFeatureStyle(check.type); + if (fcol instanceof Color) + { + new UserDefinedColours(this, check.type, (Color) fcol); + } + else + { + new FeatureColourChooser(this, check.type); + // write back the current colour object to update the table + check.updateColor(fr.getFeatureStyle(check.type)); + } } } @@ -540,21 +651,105 @@ public class FeatureSettings extends Panel implements ItemListener, class MyCheckbox extends Checkbox { + public String type; + public int stringWidth; boolean hasLink; + GraduatedColor gcol; + + Color col; + + public void updateColor(Object newcol) + { + if (newcol instanceof Color) + { + col = (Color) newcol; + gcol = null; + } + else if (newcol instanceof GraduatedColor) + { + gcol = (GraduatedColor) newcol; + col = null; + } + else + { + throw new Error("Invalid color for MyCheckBox"); + } + if (col != null) + { + setBackground(col); + } + else + { + String vlabel = type; + if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD) + { + vlabel += " " + + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)" + : "(<)"); + } + if (gcol.isColourByLabel()) + { + setBackground(Color.white); + vlabel += " (by Label)"; + } + else + { + setBackground(gcol.getMinColor()); + } + this.setLabel(vlabel); + } + repaint(); + } + public MyCheckbox(String label, boolean checked, boolean haslink) { super(label, checked); - + type = label; FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont()); stringWidth = fm.stringWidth(label); this.hasLink = haslink; } + public MyCheckbox(String type, boolean selected, boolean b, + Object featureStyle) + { + this(type, selected, b); + updateColor(featureStyle); + } + public void paint(Graphics g) { + Dimension d = getSize(); + if (gcol != null) + { + if (gcol.isColourByLabel()) + { + g.setColor(Color.white); + g.fillRect(d.width / 2, 0, d.width / 2, d.height); + /* + * g.setColor(Color.black); Font f=g.getFont().deriveFont(9); + * g.setFont(f); + * + * // g.setFont(g.getFont().deriveFont( // + * AffineTransform.getScaleInstance( // + * width/g.getFontMetrics().stringWidth("Label"), // + * height/g.getFontMetrics().getHeight()))); g.drawString("Label", + * width/2, 0); + */ + + } + else + { + Color maxCol = gcol.getMaxColor(); + g.setColor(maxCol); + g.fillRect(d.width / 2, 0, d.width / 2, d.height); + + } + } + if (hasLink) { g.drawImage(linkImage, stringWidth + 25, @@ -562,4 +757,82 @@ public class FeatureSettings extends Panel implements ItemListener, } } } + + protected void sortByDens(String[] typ) + { + sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY); + } + + private String[] getDisplayedFeatureTypes() + { + String[] typ = null; + if (fr != null) + { + synchronized (fr.renderOrder) + { + typ = new String[fr.renderOrder.length]; + System.arraycopy(fr.renderOrder, 0, typ, 0, typ.length); + for (int i = 0; i < typ.length; i++) + { + if (av.featuresDisplayed.get(typ[i]) == null) + { + typ[i] = null; + } + } + } + } + return typ; + } + + protected void sortBy(String[] typ, String methodText, final String method) + { + if (typ == null) + { + typ = getDisplayedFeatureTypes(); + } + String gps[] = null; + gps = fr.getGroups(true); + if (typ != null) + { + for (int i = 0; i < typ.length; i++) + { + System.err.println("Sorting on Types:" + typ[i]); + } + } + if (gps != null) + { + + for (int i = 0; i < gps.length; i++) + { + System.err.println("Sorting on groups:" + gps[i]); + } + } + AlignmentPanel alignPanel = ap; + AlignmentI al = alignPanel.av.getAlignment(); + + int start, stop; + SequenceGroup sg = alignPanel.av.getSelectionGroup(); + if (sg != null) + { + start = sg.getStartRes(); + stop = sg.getEndRes(); + } + else + { + start = 0; + stop = al.getWidth(); + } + SequenceI[] oldOrder = al.getSequencesArray(); + AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method); + this.ap.alignFrame.addHistoryItem(new OrderCommand(methodText, + oldOrder, alignPanel.av.getAlignment())); + alignPanel.paintAlignment(true); + + } + + protected void sortByScore(String[] typ) + { + sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE); + } + }