X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=d664cad2d30ebae2716febb873e75b20f88e195c;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=f2e44f514d2ea0cca356a7f0ebc133daa79f61cd;hpb=9c8561a294fb638ae78c01a440a863b05db2bdee;p=jalview.git diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java index f2e44f5..d664cad 100755 --- a/src/jalview/appletgui/FeatureSettings.java +++ b/src/jalview/appletgui/FeatureSettings.java @@ -1,20 +1,19 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.appletgui; @@ -23,21 +22,34 @@ 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, AdjustmentListener +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) @@ -48,7 +60,7 @@ public class FeatureSettings fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); transparency = new Scrollbar(Scrollbar.HORIZONTAL, - 100 - (int) (fr.transparency * 100), 1, 1, 100); + 100 - (int) (fr.transparency * 100), 1, 1, 100); if (fr.transparencySetter != null) { @@ -95,8 +107,9 @@ public class FeatureSettings } else { - tPanel.add(new Label("Transparency not available in this web browser"), - BorderLayout.CENTER); + tPanel.add( + new Label("Transparency not available in this web browser"), + BorderLayout.CENTER); } lowerPanel.add(tPanel, BorderLayout.SOUTH); @@ -105,8 +118,8 @@ public class FeatureSettings if (groupPanel != null) { - groupPanel.setLayout( - new GridLayout(fr.featureGroups.size() / 4 + 1, 4)); + groupPanel.setLayout(new GridLayout(fr.featureGroups.size() / 4 + 1, + 4)); groupPanel.validate(); add(groupPanel, BorderLayout.NORTH); @@ -118,22 +131,21 @@ public class FeatureSettings { public void windowClosing(WindowEvent e) { - if (me.av.featureSettings==me) + 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); + height); } public void paint(Graphics g) @@ -144,16 +156,96 @@ public class FeatureSettings 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(); if (alignmentHasFeatures) { rebuildGroups(); - + } resetTable(false); } + /** * rebuilds the group panel */ @@ -163,21 +255,21 @@ public class FeatureSettings if (groupPanel == null) { groupPanel = new Panel(); - } else { + } + 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)) - ); + 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); @@ -189,8 +281,8 @@ public class FeatureSettings } } - //This routine adds and removes checkboxes depending on - //Group selection states + // This routine adds and removes checkboxes depending on + // Group selection states void resetTable(boolean groupsChanged) { SequenceFeature[] tmpfeatures; @@ -210,8 +302,8 @@ public class FeatureSettings { group = tmpfeatures[index].featureGroup; - if (group == null || fr.featureGroups.get(group) == null || - ( (Boolean) fr.featureGroups.get(group)).booleanValue()) + if (group == null || fr.featureGroups.get(group) == null + || ((Boolean) fr.featureGroups.get(group)).booleanValue()) { type = tmpfeatures[index].getType(); if (!visibleChecks.contains(type)) @@ -225,14 +317,14 @@ public class FeatureSettings Component[] comps; int cSize = featurePanel.getComponentCount(); - Checkbox check; - //This will remove any checkboxes which shouldn't be - //visible + 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--; @@ -242,8 +334,8 @@ public class FeatureSettings if (fr.renderOrder != null) { - //First add the checks in the previous render order, - //in case the window has been closed and reopened + // 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]; @@ -268,8 +360,8 @@ public class FeatureSettings addCheck(groupsChanged, en.nextElement().toString()); } - featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(), 1, - 10, 5)); + featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(), + 1, 10, 5)); featurePanel.validate(); if (scrollPane != null) @@ -279,21 +371,26 @@ public class FeatureSettings 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. + * + * @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; + 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; @@ -308,17 +405,25 @@ public class FeatureSettings selected = true; } - check = new MyCheckbox(type, - selected, - (fr.featureLinks != null && - fr.featureLinks.containsKey(type)) - ); + check = new MyCheckbox( + type, + selected, + (fr.featureLinks != null && fr.featureLinks.containsKey(type)), + fr.getFeatureStyle(type)); check.addMouseListener(this); check.addMouseMotionListener(this); - check.setBackground(fr.getColour(type)); check.addItemListener(this); - featurePanel.add(check); + if (groupsChanged) + { + // add at beginning of stack. + featurePanel.add(check, 0); + } + else + { + // add at end of stack. + featurePanel.add(check); + } } } @@ -336,11 +441,12 @@ public class FeatureSettings { if (evt != null) { - //Is the source a top level featureGroup? + // 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())); + fr.featureGroups.put(source.getLabel(), new Boolean(source + .getState())); ap.seqPanel.seqCanvas.repaint(); if (ap.overviewPanel != null) { @@ -363,9 +469,9 @@ public class FeatureSettings 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++; } @@ -379,6 +485,7 @@ public class FeatureSettings } MyCheckbox selectedCheck; + boolean dragging = false; public void mousePressed(MouseEvent evt) @@ -387,8 +494,7 @@ public class FeatureSettings selectedCheck = (MyCheckbox) evt.getSource(); if (fr.featureLinks != null - && fr.featureLinks.containsKey(selectedCheck.getLabel()) - ) + && fr.featureLinks.containsKey(selectedCheck.type)) { if (evt.getX() > selectedCheck.stringWidth + 20) { @@ -400,7 +506,7 @@ public class FeatureSettings public void mouseDragged(MouseEvent evt) { - if ( ( (Component) evt.getSource()).getParent() != featurePanel) + if (((Component) evt.getSource()).getParent() != featurePanel) { return; } @@ -409,7 +515,7 @@ public class FeatureSettings public void mouseReleased(MouseEvent evt) { - if ( ( (Component) evt.getSource()).getParent() != featurePanel) + if (((Component) evt.getSource()).getParent() != featurePanel) { return; } @@ -422,7 +528,8 @@ public class FeatureSettings if (height > featurePanel.getSize().height) { - comp = featurePanel.getComponent(featurePanel.getComponentCount() - 1); + comp = featurePanel + .getComponent(featurePanel.getComponentCount() - 1); } else if (height < 0) { @@ -430,9 +537,8 @@ public class FeatureSettings } else { - comp = featurePanel.getComponentAt(evt.getX(), - evt.getY() + - evt.getComponent().getLocation().y); + comp = featurePanel.getComponentAt(evt.getX(), evt.getY() + + evt.getComponent().getLocation().y); } if (comp != null && comp instanceof Checkbox) @@ -440,9 +546,7 @@ public class FeatureSettings target = (Checkbox) comp; } - if (selectedCheck != null - && target != null - && selectedCheck != target) + if (selectedCheck != null && target != null && selectedCheck != target) { int targetIndex = -1; for (int i = 0; i < featurePanel.getComponentCount(); i++) @@ -461,33 +565,51 @@ public class FeatureSettings } } - 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); } 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.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("|"))); } } @@ -498,43 +620,215 @@ public class FeatureSettings 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)); + } } } public void mouseMoved(MouseEvent evt) - {} + { + } public void adjustmentValueChanged(AdjustmentEvent evt) { - fr.transparency = ( (float) (100 - transparency.getValue()) / 100f); + fr.transparency = ((float) (100 - transparency.getValue()) / 100f); ap.seqPanel.seqCanvas.repaint(); } - class MyCheckbox - extends Checkbox + 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, ( - getSize().height - linkImage.getHeight(this)) / 2, - this); + g.drawImage(linkImage, stringWidth + 25, + (getSize().height - linkImage.getHeight(this)) / 2, this); } } } + + 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); + } + }