X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=9b2dba671aecb94262ad65ed6367d3937f500f53;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=a733e24c1763300c9d01178fa804cf859b145c86;hpb=bceadbb394604c88ac18e2dcf4b33e735377d7ac;p=jalview.git diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java index a733e24..9b2dba6 100755 --- a/src/jalview/appletgui/FeatureSettings.java +++ b/src/jalview/appletgui/FeatureSettings.java @@ -1,509 +1,834 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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 jalview.datamodel.*; -import java.awt.*; -import java.util.*; -import java.awt.event.*; - - -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(AlignViewport av, final AlignmentPanel ap) - { - this.ap = ap; - this.av = 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 +30; - - height = Math.max(100, 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); - } - - 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; iselectedCheck.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 > this.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 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 (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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; + +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 +{ + 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); + } + + 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 + */ + 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(); + MyCheckbox check; + // This will remove any checkboxes which shouldn't be + // visible + for (int i = 0; i < cSize; i++) + { + comps = featurePanel.getComponents(); + check = (MyCheckbox) comps[i]; + if (!visibleChecks.contains(check.type)) + { + 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(); + MyCheckbox check; + addCheck = true; + for (int i = 0; i < featurePanel.getComponentCount(); i++) + { + check = (MyCheckbox) comps[i]; + if (check.type.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)), + fr.getFeatureStyle(type)); + + check.addMouseListener(this); + check.addMouseMotionListener(this); + check.addItemListener(this); + if (groupsChanged) + { + // add at beginning of stack. + featurePanel.add(check, 0); + } + else + { + // add at end of stack. + 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++) + { + 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++; + } + + 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.type)) + { + 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, 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() + { + 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 ((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.type).toString(); + ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1), + link.substring(0, link.indexOf("|"))); + } + } + + if (check.getParent() != featurePanel) + { + return; + } + + if (evt.getClickCount() > 1) + { + 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); + ap.seqPanel.seqCanvas.repaint(); + + } + + 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); + } + } + } + + 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); + } + +}