X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=955684c7cd175bfe919052d3e63ea2a8f7f4e8fc;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=7acd374c4266f59b3e040d3f048945c6f40c4839;hpb=4e2a76c531103d213482fb4969da33287d35411b;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 7acd374..955684c 100755 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * 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 @@ -18,21 +18,20 @@ */ package jalview.gui; -import jalview.datamodel.*; -import javax.swing.*; -import javax.swing.event.*; -import java.awt.*; +import java.io.*; import java.util.*; -import javax.swing.BorderFactory; + +import java.awt.*; import java.awt.event.*; +import javax.swing.*; +import javax.swing.event.*; import javax.swing.table.*; -import java.io.*; -import jalview.io.JalviewFileChooser; -import java.awt.BorderLayout; -import java.awt.Font; -import java.awt.Color; -public class FeatureSettings extends JPanel +import jalview.datamodel.*; +import jalview.io.*; + +public class FeatureSettings + extends JPanel { DasSourceBrowser dassourceBrowser; jalview.io.DasSequenceFeatureFetcher dasFeatureFetcher; @@ -41,7 +40,7 @@ public class FeatureSettings extends JPanel final FeatureRenderer fr; public final AlignFrame af; - Object [][] originalData; + Object[][] originalData; final JInternalFrame frame; JScrollPane scrollPane = new JScrollPane(); JTable table; @@ -55,72 +54,72 @@ public class FeatureSettings extends JPanel this.af = af; fr = af.getFeatureRenderer(); - transparency.setMaximum( 100 - (int)(fr.transparency*100) ) ; - - try - { - jbInit(); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - - table = new JTable(); - table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12)); - table.setFont(new Font("Verdana", Font.PLAIN, 12)); - table.setDefaultRenderer(Color.class, - new ColorRenderer()); - - table.setDefaultEditor(Color.class, - new ColorEditor()); - - table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); - - table.addMouseListener(new MouseAdapter() - { - public void mousePressed(MouseEvent evt) - { - selectedRow = table.rowAtPoint(evt.getPoint()); - } - }); - - table.addMouseMotionListener(new MouseMotionAdapter() - { - public void mouseDragged(MouseEvent evt) - { - int newRow = table.rowAtPoint(evt.getPoint()); - if (newRow != selectedRow - && selectedRow != -1 - && newRow != -1) - { - Object[] temp = new Object[3]; - temp[0] = table.getValueAt(selectedRow, 0); - temp[1] = table.getValueAt(selectedRow, 1); - temp[2] = table.getValueAt(selectedRow, 2); - - table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0); - table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1); - table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2); - - table.setValueAt(temp[0], newRow, 0); - table.setValueAt(temp[1], newRow, 1); - table.setValueAt(temp[2], newRow, 2); - - selectedRow = newRow; - } - } - }); - - scrollPane.setViewportView(table); + transparency.setMaximum(100 - (int) (fr.transparency * 100)); - dassourceBrowser = new DasSourceBrowser(); - dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER); + try + { + jbInit(); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + table = new JTable(); + table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12)); + table.setFont(new Font("Verdana", Font.PLAIN, 12)); + table.setDefaultRenderer(Color.class, + new ColorRenderer()); + table.setDefaultEditor(Color.class, + new ColorEditor()); - if (af.getViewport().featuresDisplayed == null || fr.renderOrder==null) - fr.findAllFeatures(); + table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); + + table.addMouseListener(new MouseAdapter() + { + public void mousePressed(MouseEvent evt) + { + selectedRow = table.rowAtPoint(evt.getPoint()); + } + }); + + table.addMouseMotionListener(new MouseMotionAdapter() + { + public void mouseDragged(MouseEvent evt) + { + int newRow = table.rowAtPoint(evt.getPoint()); + if (newRow != selectedRow + && selectedRow != -1 + && newRow != -1) + { + Object[] temp = new Object[3]; + temp[0] = table.getValueAt(selectedRow, 0); + temp[1] = table.getValueAt(selectedRow, 1); + temp[2] = table.getValueAt(selectedRow, 2); + + table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0); + table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1); + table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2); + + table.setValueAt(temp[0], newRow, 0); + table.setValueAt(temp[1], newRow, 1); + table.setValueAt(temp[2], newRow, 2); + + selectedRow = newRow; + } + } + }); + + scrollPane.setViewportView(table); + + dassourceBrowser = new DasSourceBrowser(); + dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER); + + if (af.getViewport().featuresDisplayed == null || fr.renderOrder == null) + { + fr.findAllFeatures(); + } setTableData(); @@ -133,7 +132,9 @@ public class FeatureSettings extends JPanel synchronized public void setTableData() { if (fr.featureGroups == null) + { fr.featureGroups = new Hashtable(); + } Vector allFeatures = new Vector(); Vector allGroups = new Vector(); @@ -142,151 +143,164 @@ public class FeatureSettings extends JPanel for (int i = 0; i < af.getViewport().alignment.getHeight(); i++) { - if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null) + if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence(). + getSequenceFeatures() == null) + { continue; + } - tmpfeatures = af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures(); + tmpfeatures = af.getViewport().alignment.getSequenceAt(i). + getDatasetSequence().getSequenceFeatures(); int index = 0; while (index < tmpfeatures.length) { - if(tmpfeatures[index].begin == 0 && tmpfeatures[index].end ==0) + if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0) { index++; continue; } - if(tmpfeatures[index].getFeatureGroup()!=null) + 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(); - } - - if (groupPanel == null) - { - groupPanel = new JPanel(); - } - - boolean alreadyAdded = false; - for(int g=0; g-1; ro--) + for (int ro = fr.renderOrder.length - 1; ro > -1; ro--) { - type = fr.renderOrder[ro]; + type = fr.renderOrder[ro]; - if(!visibleChecks.contains(type)) - continue; + if (!visibleChecks.contains(type)) + { + continue; + } - data[dataIndex][0] = type; - data[dataIndex][1] = fr.getColour(type); - data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed.containsKey(type)); - dataIndex++; - visibleChecks.removeElement(type); + data[dataIndex][0] = type; + data[dataIndex][1] = fr.getColour(type); + data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed. + containsKey(type)); + dataIndex++; + visibleChecks.removeElement(type); } } fSize = visibleChecks.size(); - for(int i=0; i0) + if (af.getViewport().getSelectionGroup() != null + && af.getViewport().getSelectionGroup().getSize() > 0) { - iSize = af.getViewport().getSelectionGroup().getSize(false); + iSize = af.getViewport().getSelectionGroup().getSize(); dataset = new SequenceI[iSize]; seqs = af.getViewport().getSelectionGroup(). getSequencesInOrder( @@ -589,8 +610,8 @@ public class FeatureSettings extends JPanel } else { - iSize = af.getViewport().getAlignment().getHeight(); - seqs = af.getViewport().getAlignment().getSequencesArray(); + iSize = af.getViewport().getAlignment().getHeight(); + seqs = af.getViewport().getAlignment().getSequencesArray(); } dataset = new SequenceI[iSize]; @@ -601,9 +622,9 @@ public class FeatureSettings extends JPanel dasFeatureFetcher = new jalview.io.DasSequenceFeatureFetcher( - dataset, - this, - selectedSources); + dataset, + this, + selectedSources); af.getViewport().setShowSequenceFeatures(true); af.showSeqFeatures.setSelected(true); @@ -638,153 +659,179 @@ public class FeatureSettings extends JPanel this.data = data; } - private String[] columnNames = {"Feature Type", "Colour","Display"}; - private Object[][] data; + private String[] columnNames = + { + "Feature Type", "Colour", "Display"}; + private Object[][] data; - public Object[][] getData() - { - return data; - } + public Object[][] getData() + { + return data; + } - public void setData(Object[][] data) - { - this.data = data; - } + public void setData(Object[][] data) + { + this.data = data; + } - public int getColumnCount() { - return columnNames.length; - } + public int getColumnCount() + { + return columnNames.length; + } - public Object[] getRow(int row) - { - return data[row]; - } + public Object[] getRow(int row) + { + return data[row]; + } - public int getRowCount() { - return data.length; - } + public int getRowCount() + { + return data.length; + } - public String getColumnName(int col) { - return columnNames[col]; - } + public String getColumnName(int col) + { + return columnNames[col]; + } - public Object getValueAt(int row, int col) { - return data[row][col]; - } + public Object getValueAt(int row, int col) + { + return data[row][col]; + } - public Class getColumnClass(int c) { - return getValueAt(0, c).getClass(); - } + public Class getColumnClass(int c) + { + return getValueAt(0, c).getClass(); + } - public boolean isCellEditable(int row, int col) { - return col==0 ? false:true; - } + public boolean isCellEditable(int row, int col) + { + return col == 0 ? false : true; + } - public void setValueAt(Object value, int row, int col) { - data[row][col] = value; - fireTableCellUpdated(row, col); - updateFeatureRenderer(data); - } + public void setValueAt(Object value, int row, int col) + { + data[row][col] = value; + fireTableCellUpdated(row, col); + updateFeatureRenderer(data); + } + + } + class ColorRenderer + extends JLabel implements TableCellRenderer + { + javax.swing.border.Border unselectedBorder = null; + javax.swing.border.Border selectedBorder = null; + + public ColorRenderer() + { + setOpaque(true); //MUST do this for background to show up. } - class ColorRenderer extends JLabel - implements TableCellRenderer { - javax.swing.border.Border unselectedBorder = null; - javax.swing.border.Border selectedBorder = null; - - public ColorRenderer() { - setOpaque(true); //MUST do this for background to show up. - } - - public Component getTableCellRendererComponent( - JTable table, Object color, - boolean isSelected, boolean hasFocus, - int row, int column) { - Color newColor = (Color)color; - setBackground(newColor); - if (isSelected) { - if (selectedBorder == null) { - selectedBorder = BorderFactory.createMatteBorder(2,5,2,5, - table.getSelectionBackground()); - } - setBorder(selectedBorder); - } else { - if (unselectedBorder == null) { - unselectedBorder = BorderFactory.createMatteBorder(2,5,2,5, - table.getBackground()); - } - setBorder(unselectedBorder); - } - - setToolTipText("RGB value: " + newColor.getRed() + ", " - + newColor.getGreen() + ", " - + newColor.getBlue()); - return this; - } - } + + public Component getTableCellRendererComponent( + JTable table, Object color, + boolean isSelected, boolean hasFocus, + int row, int column) + { + Color newColor = (Color) color; + setBackground(newColor); + if (isSelected) + { + if (selectedBorder == null) + { + selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, + table.getSelectionBackground()); + } + setBorder(selectedBorder); + } + else + { + if (unselectedBorder == null) + { + unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, + table.getBackground()); + } + setBorder(unselectedBorder); + } + + setToolTipText("RGB value: " + newColor.getRed() + ", " + + newColor.getGreen() + ", " + + newColor.getBlue()); + return this; + } + } } - class ColorEditor extends AbstractCellEditor - implements TableCellEditor, - ActionListener { - Color currentColor; - JButton button; - JColorChooser colorChooser; - JDialog dialog; - protected static final String EDIT = "edit"; - - public ColorEditor() { - //Set up the editor (from the table's point of view), - //which is a button. - //This button brings up the color chooser dialog, - //which is the editor from the user's point of view. - button = new JButton(); - button.setActionCommand(EDIT); - button.addActionListener(this); - button.setBorderPainted(false); - //Set up the dialog that the button brings up. - colorChooser = new JColorChooser(); - dialog = JColorChooser.createDialog(button, - "Select new Colour", - true, //modal - colorChooser, - this, //OK button handler - null); //no CANCEL button handler - } - - /** - * Handles events from the editor button and from - * the dialog's OK button. - */ - public void actionPerformed(ActionEvent e) { - - if (EDIT.equals(e.getActionCommand())) { - //The user has clicked the cell, so - //bring up the dialog. - button.setBackground(currentColor); - colorChooser.setColor(currentColor); - dialog.setVisible(true); - - //Make the renderer reappear. - fireEditingStopped(); - - } else { //User pressed dialog's "OK" button. - currentColor = colorChooser.getColor(); - } - } - - //Implement the one CellEditor method that AbstractCellEditor doesn't. - public Object getCellEditorValue() { - return currentColor; - } - - //Implement the one method defined by TableCellEditor. - public Component getTableCellEditorComponent(JTable table, - Object value, - boolean isSelected, - int row, - int column) { - currentColor = (Color)value; - return button; - } +class ColorEditor + extends AbstractCellEditor implements TableCellEditor, + ActionListener +{ + Color currentColor; + JButton button; + JColorChooser colorChooser; + JDialog dialog; + protected static final String EDIT = "edit"; + + public ColorEditor() + { + //Set up the editor (from the table's point of view), + //which is a button. + //This button brings up the color chooser dialog, + //which is the editor from the user's point of view. + button = new JButton(); + button.setActionCommand(EDIT); + button.addActionListener(this); + button.setBorderPainted(false); + //Set up the dialog that the button brings up. + colorChooser = new JColorChooser(); + dialog = JColorChooser.createDialog(button, + "Select new Colour", + true, //modal + colorChooser, + this, //OK button handler + null); //no CANCEL button handler + } + + /** + * Handles events from the editor button and from + * the dialog's OK button. + */ + public void actionPerformed(ActionEvent e) + { + + if (EDIT.equals(e.getActionCommand())) + { + //The user has clicked the cell, so + //bring up the dialog. + button.setBackground(currentColor); + colorChooser.setColor(currentColor); + dialog.setVisible(true); + + //Make the renderer reappear. + fireEditingStopped(); + + } + else + { //User pressed dialog's "OK" button. + currentColor = colorChooser.getColor(); + } + } + + //Implement the one CellEditor method that AbstractCellEditor doesn't. + public Object getCellEditorValue() + { + return currentColor; + } + + //Implement the one method defined by TableCellEditor. + public Component getTableCellEditorComponent(JTable table, + Object value, + boolean isSelected, + int row, + int column) + { + currentColor = (Color) value; + return button; + } }