-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.appletgui;\r
-\r
-import jalview.datamodel.*;\r
-import java.awt.*;\r
-import java.util.*;\r
-import java.awt.event.*;\r
-\r
-\r
-public class FeatureSettings extends Panel implements ItemListener,\r
- MouseListener, MouseMotionListener\r
-{\r
- final FeatureRenderer fr;\r
- final AlignmentPanel ap;\r
- final AlignViewport av;\r
- final Frame frame;\r
-\r
- public FeatureSettings(AlignViewport av, final AlignmentPanel ap)\r
- {\r
- this.ap = ap;\r
- this.av = av;\r
- fr = ap.seqPanel.seqCanvas.getFeatureRenderer();\r
-\r
- setTableData();\r
-\r
- frame = new Frame();\r
- frame.add(this);\r
- int height = this.getComponentCount()*50;\r
- if (height>400)\r
- height = 400;\r
-\r
- jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", 200,\r
- height);\r
- }\r
-\r
- void setTableData()\r
- {\r
- Vector allFeatures = new Vector();\r
- Vector features;\r
- Enumeration e;\r
- SequenceFeature sf;\r
-\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- features = av.alignment.getSequenceAt(i).getSequenceFeatures();\r
- if (features == null)\r
- continue;\r
-\r
- e = features.elements();\r
- while (e.hasMoreElements())\r
- {\r
- sf = (SequenceFeature) e.nextElement();\r
- if (!allFeatures.contains(sf.getType()))\r
- {\r
- allFeatures.addElement(sf.getType());\r
- }\r
- }\r
- }\r
-\r
- int fSize = allFeatures.size();\r
-\r
- String type;\r
- this.setLayout(new GridLayout(fSize, 2, 10,5));\r
-\r
- for (int i = 0; i < fSize; i++)\r
- {\r
- type = allFeatures.elementAt(i).toString();\r
- Color col = fr.getColour(type);\r
- boolean displayed = true;\r
- if(fr.featuresDisplayed!=null)\r
- displayed = fr.featuresDisplayed.contains(type);\r
-\r
- Checkbox check = new Checkbox(type, displayed);\r
- check.addMouseListener(this);\r
- check.addMouseMotionListener(this);\r
- check.setBackground(col);\r
- check.addItemListener(this);\r
- add(check);\r
- }\r
- validate();\r
- }\r
-\r
- public void itemStateChanged(ItemEvent evt)\r
- {\r
- Component [] comps = this.getComponents();\r
- int cSize = comps.length;\r
-\r
- Object [][] data = new Object[cSize][3];\r
-\r
- for(int i=0; i<cSize; i++)\r
- {\r
- Checkbox check = (Checkbox)comps[i];\r
- data[i][0] = check.getLabel();\r
- data[i][1] = fr.getColour(check.getLabel());\r
- data[i][2] = new Boolean(check.getState());\r
- }\r
-\r
- fr.setFeaturePriority(data);\r
- ap.seqPanel.seqCanvas.repaint();\r
- }\r
-\r
- Checkbox selectedCheck;\r
- boolean dragging = false;\r
-\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- selectedCheck = (Checkbox)evt.getSource();\r
- }\r
-\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- dragging = true;\r
- }\r
-\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- Component comp = null;\r
- Checkbox target = null;\r
-\r
- int height = evt.getY()+evt.getComponent().getLocation().y;\r
-\r
- if(height > this.getSize().height)\r
- {\r
- comp = this.getComponent(this.getComponentCount()-1);\r
- }\r
- else if(height < 0)\r
- {\r
- comp = this.getComponent(0);\r
- }\r
- else\r
- {\r
- comp = this.getComponentAt(evt.getX(),\r
- evt.getY() +\r
- evt.getComponent().getLocation().y);\r
- }\r
-\r
- if(comp!=null && comp instanceof Checkbox)\r
- target = (Checkbox)comp;\r
-\r
- if (selectedCheck != null && target != null && selectedCheck != target)\r
- {\r
- int targetIndex = -1;\r
- for(int i=0; i<this.getComponentCount(); i++)\r
- {\r
- if(target==this.getComponent(i))\r
- { targetIndex = i; break; }\r
- }\r
-\r
-\r
- this.remove(selectedCheck);\r
- this.add(selectedCheck, targetIndex);\r
- validate();\r
- }\r
- }\r
-\r
-\r
- public void mouseEntered(MouseEvent evt){}\r
- public void mouseExited(MouseEvent evt){}\r
- public void mouseClicked(MouseEvent evt){}\r
- public void mouseMoved(MouseEvent evt){}\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+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);
+ 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++)
+ {
+ 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);
+ }
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff