--- /dev/null
+package jalview.appletgui;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.gui.JvSwingUtils;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.util.MessageManager;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+
+import java.awt.BorderLayout;
+import java.awt.CardLayout;
+import java.awt.Checkbox;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Frame;
+import java.awt.Panel;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.TextEvent;
+import java.awt.event.TextListener;
+import java.util.Iterator;
+import java.util.Vector;
+
+import net.miginfocom.swing.MigLayout;
+
+public class AnnotationColumnChooser extends AnnotationRowFilter implements
+ ActionListener, AdjustmentListener, ItemListener, MouseListener
+{
+
+ private Choice annotations = new Choice();
+
+ private Panel actionPanel = new Panel();
+
+ private TitledPanel thresholdPanel = new TitledPanel();
+
+ private Panel switchableViewsPanel = new Panel(new CardLayout());
+
+ private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
+ .getLayout());
+
+ private Panel noGraphFilterView = new Panel();
+
+ private Panel graphFilterView = new Panel();
+
+ private Panel annotationComboBoxPanel = new Panel();
+
+ private BorderLayout borderLayout1 = new BorderLayout();
+
+ private Choice threshold = new Choice();
+
+ private StructureFilterPanel gStructureFilterPanel;
+
+ private StructureFilterPanel ngStructureFilterPanel;
+
+ private StructureFilterPanel currentStructureFilterPanel;
+
+ private SearchPanel currentSearchPanel;
+
+ private SearchPanel gSearchPanel;
+
+ private SearchPanel ngSearchPanel;
+
+ private FurtherActionPanel currentFurtherActionPanel;
+
+ private FurtherActionPanel gFurtherActionPanel;
+
+ private FurtherActionPanel ngFurtherActionPanel;
+
+ public static final int ACTION_OPTION_SELECT = 1;
+
+ public static int ACTION_OPTION_HIDE = 2;
+
+ public static String NO_GRAPH_VIEW = "0";
+
+ public static String GRAPH_VIEW = "1";
+
+ private int actionOption = ACTION_OPTION_SELECT;
+
+ private ColumnSelection oldColumnSelection;
+
+ public AnnotationColumnChooser()
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
+ {
+ super(av, ap);
+ frame = new Frame();
+ frame.add(this);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.select_by_annotation"), 520,
+ 215);
+
+ slider.addAdjustmentListener(this);
+ slider.addMouseListener(this);
+
+ if (av.getAlignment().getAlignmentAnnotation() == null)
+ {
+ return;
+ }
+ setOldColumnSelection(av.getColumnSelection());
+ adjusting = true;
+ Vector list = new Vector();
+ int index = 1;
+ for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+ {
+ String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+ if (!list.contains(label))
+ {
+ list.addElement(label);
+ }
+ else
+ {
+ list.addElement(label + "_" + (index++));
+ }
+ }
+
+ for (int i = 0; i < list.size(); i++)
+ {
+ annotations.addItem(list.elementAt(i).toString());
+ }
+
+ populateThresholdComboBox(threshold);
+
+ // restore Object state from the previous session if one exists
+ if (av.getAnnotationColumnSelectionState() != null)
+ {
+ currentSearchPanel = av.getAnnotationColumnSelectionState()
+ .getCurrentSearchPanel();
+ currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
+ .getCurrentStructureFilterPanel();
+ annotations.select(av.getAnnotationColumnSelectionState()
+ .getAnnotations().getSelectedIndex());
+ threshold.select(av.getAnnotationColumnSelectionState()
+ .getThreshold().getSelectedIndex());
+ actionOption = av.getAnnotationColumnSelectionState()
+ .getActionOption();
+ }
+
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ }
+ adjusting = false;
+
+ updateView();
+ frame.invalidate();
+ frame.pack();
+ }
+
+ private void jbInit() throws Exception
+ {
+ ok.setLabel(MessageManager.getString("action.ok"));
+
+ cancel.setLabel(MessageManager.getString("action.cancel"));
+
+ thresholdValue.setEnabled(false);
+ thresholdValue.setColumns(7);
+
+ ok.addActionListener(this);
+ cancel.addActionListener(this);
+ annotations.addItemListener(this);
+ thresholdValue.addActionListener(this);
+ threshold.addItemListener(this);
+
+ slider.setBackground(Color.white);
+ slider.setEnabled(false);
+ slider.setPreferredSize(new Dimension(100, 32));
+
+ thresholdPanel.setBackground(Color.white);
+ thresholdPanel.setFont(JvSwingUtils.getLabelFont());
+ thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
+
+ actionPanel.setBackground(Color.white);
+ actionPanel.setFont(JvSwingUtils.getLabelFont());
+
+ graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
+ graphFilterView.setBackground(Color.white);
+
+ noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
+ noGraphFilterView.setBackground(Color.white);
+
+ annotationComboBoxPanel.setBackground(Color.white);
+ annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
+
+ gSearchPanel = new SearchPanel(this);
+ ngSearchPanel = new SearchPanel(this);
+ gFurtherActionPanel = new FurtherActionPanel(this);
+ ngFurtherActionPanel = new FurtherActionPanel(this);
+ gStructureFilterPanel = new StructureFilterPanel(this);
+ ngStructureFilterPanel = new StructureFilterPanel(this);
+
+ thresholdPanel.setTitle("Threshold Filter");
+ thresholdPanel.add(getThreshold(), "grow");
+ thresholdPanel.add(thresholdValue, "grow, wrap");
+ thresholdPanel.add(slider, "grow, span, wrap");
+
+ actionPanel.add(ok);
+ actionPanel.add(cancel);
+
+ graphFilterView.add(gSearchPanel, "grow, span, wrap");
+ graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
+ graphFilterView.add(thresholdPanel, "grow, span, wrap");
+ graphFilterView.add(gFurtherActionPanel);
+
+ noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
+ noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
+ noGraphFilterView.add(ngFurtherActionPanel);
+
+ annotationComboBoxPanel.add(getAnnotations());
+ switchableViewsPanel.add(noGraphFilterView,
+ AnnotationColumnChooser.NO_GRAPH_VIEW);
+ switchableViewsPanel.add(graphFilterView,
+ AnnotationColumnChooser.GRAPH_VIEW);
+
+ this.setLayout(borderLayout1);
+ this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
+ this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
+ this.add(actionPanel, java.awt.BorderLayout.SOUTH);
+
+ selectedAnnotationChanged();
+ this.validate();
+ }
+
+ @SuppressWarnings("unchecked")
+ public void reset()
+ {
+ if (this.getOldColumnSelection() != null)
+ {
+ av.getColumnSelection().clear();
+
+ if (av.getAnnotationColumnSelectionState() != null)
+ {
+ ColumnSelection oldSelection = av
+ .getAnnotationColumnSelectionState()
+ .getOldColumnSelection();
+ if (oldSelection != null && oldSelection.getHiddenColumns() != null
+ && !oldSelection.getHiddenColumns().isEmpty())
+ {
+ for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
+ .iterator(); itr.hasNext();)
+ {
+ int positions[] = itr.next();
+ av.hideColumns(positions[0], positions[1]);
+ }
+ }
+ av.setColumnSelection(oldSelection);
+ }
+ ap.paintAlignment(true);
+ }
+
+ }
+
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+ if (!adjusting)
+ {
+ thresholdValue.setText((slider.getValue() / 1000f) + "");
+ valueChanged(!sliderDragging);
+ }
+ }
+
+ protected void addSliderMouseListeners()
+ {
+
+ slider.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ sliderDragging = true;
+ super.mousePressed(e);
+ }
+
+ @Override
+ public void mouseDragged(MouseEvent e)
+ {
+ sliderDragging = true;
+ super.mouseDragged(e);
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (sliderDragging)
+ {
+ sliderDragging = false;
+ valueChanged(true);
+ }
+ ap.paintAlignment(true);
+ }
+ });
+ }
+
+ public void valueChanged(boolean updateAllAnnotation)
+ {
+ if (slider.isEnabled())
+ {
+ getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+ updateView();
+ ap.paintAlignment(false);
+ }
+ }
+
+ public Choice getThreshold()
+ {
+ return threshold;
+ }
+
+ public void setThreshold(Choice threshold)
+ {
+ this.threshold = threshold;
+ }
+
+ public Choice getAnnotations()
+ {
+ return annotations;
+ }
+
+ public void setAnnotations(Choice annotations)
+ {
+ this.annotations = annotations;
+ }
+
+ @Override
+ public void updateView()
+ {
+ // Check if combobox is still adjusting
+ if (adjusting)
+ {
+ return;
+ }
+
+ AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
+ setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[getAnnotations()
+ .getSelectedIndex()]);
+
+ int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
+ .getSelectedIndex());
+
+ slider.setEnabled(true);
+ thresholdValue.setEnabled(true);
+
+ if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
+ {
+ slider.setEnabled(false);
+ thresholdValue.setEnabled(false);
+ thresholdValue.setText("");
+ // build filter params
+ }
+ else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ if (getCurrentAnnotation().threshold == null)
+ {
+ getCurrentAnnotation()
+ .setThreshold(
+ new jalview.datamodel.GraphLine(
+ (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
+ "Threshold", Color.black));
+ }
+
+ adjusting = true;
+ float range = getCurrentAnnotation().graphMax * 1000
+ - getCurrentAnnotation().graphMin * 1000;
+
+ slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
+ slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
+ slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
+ thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
+ // slider.setMajorTickSpacing((int) (range / 10f));
+ slider.setEnabled(true);
+ thresholdValue.setEnabled(true);
+ adjusting = false;
+
+ // build filter params
+ filterParams
+ .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
+ if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
+ {
+ filterParams
+ .setThresholdValue(getCurrentAnnotation().threshold.value);
+
+ if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
+ {
+ filterParams
+ .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
+ }
+ else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
+ {
+ filterParams
+ .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
+ }
+ }
+ }
+
+ if (currentStructureFilterPanel != null)
+ {
+ if (currentStructureFilterPanel.alphaHelix.getState())
+ {
+ filterParams.setFilterAlphaHelix(true);
+ }
+ if (currentStructureFilterPanel.betaStrand.getState())
+ {
+ filterParams.setFilterBetaSheet(true);
+ }
+ if (currentStructureFilterPanel.turn.getState())
+ {
+ filterParams.setFilterTurn(true);
+ }
+ }
+
+ if (currentSearchPanel != null)
+ {
+
+ if (!currentSearchPanel.searchBox.getText().isEmpty())
+ {
+ currentSearchPanel.description.setEnabled(true);
+ currentSearchPanel.displayName.setEnabled(true);
+ filterParams.setRegexString(currentSearchPanel.searchBox.getText());
+ if (currentSearchPanel.displayName.getState())
+ {
+ filterParams
+ .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
+ }
+ if (currentSearchPanel.description.getState())
+ {
+ filterParams
+ .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
+ }
+ }
+ else
+ {
+ currentSearchPanel.description.setEnabled(false);
+ currentSearchPanel.displayName.setEnabled(false);
+ }
+ }
+
+ av.getColumnSelection().filterAnnotations(
+ getCurrentAnnotation().annotations, filterParams);
+
+ av.showAllHiddenColumns();
+ if (getActionOption() == ACTION_OPTION_HIDE)
+ {
+ av.hideSelectedColumns();
+ }
+
+ filterParams = null;
+ av.setAnnotationColumnSelectionState(this);
+ ap.paintAlignment(true);
+ }
+
+ public ColumnSelection getOldColumnSelection()
+ {
+ return oldColumnSelection;
+ }
+
+ public void setOldColumnSelection(ColumnSelection currentColumnSelection)
+ {
+ if (currentColumnSelection != null)
+ {
+ this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
+ }
+ }
+
+ public FurtherActionPanel getCurrentFutherActionPanel()
+ {
+ return currentFurtherActionPanel;
+ }
+
+ public void setCurrentFutherActionPanel(
+ FurtherActionPanel currentFutherActionPanel)
+ {
+ this.currentFurtherActionPanel = currentFutherActionPanel;
+ }
+
+ public SearchPanel getCurrentSearchPanel()
+ {
+ return currentSearchPanel;
+ }
+
+ public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
+ {
+ this.currentSearchPanel = currentSearchPanel;
+ }
+
+ public int getActionOption()
+ {
+ return actionOption;
+ }
+
+ public void setActionOption(int actionOption)
+ {
+ this.actionOption = actionOption;
+ }
+
+ public StructureFilterPanel getCurrentStructureFilterPanel()
+ {
+ return currentStructureFilterPanel;
+ }
+
+ public void setCurrentStructureFilterPanel(
+ StructureFilterPanel currentStructureFilterPanel)
+ {
+ this.currentStructureFilterPanel = currentStructureFilterPanel;
+ }
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (e.getSource() == annotations)
+ {
+ selectedAnnotationChanged();
+ }
+ else if (e.getSource() == threshold)
+ {
+ threshold_actionPerformed(null);
+ }
+ }
+
+ public void selectedAnnotationChanged()
+ {
+ String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
+ if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
+ .getSelectedIndex()].graph != AlignmentAnnotation.NO_GRAPH)
+ {
+ currentView = AnnotationColumnChooser.GRAPH_VIEW;
+ }
+
+ gSearchPanel.syncState();
+ gFurtherActionPanel.syncState();
+ gStructureFilterPanel.syncState();
+
+ ngSearchPanel.syncState();
+ ngFurtherActionPanel.syncState();
+ ngStructureFilterPanel.syncState();
+
+ switchableViewsLayout.show(switchableViewsPanel, currentView);
+ updateView();
+ }
+
+ public class FurtherActionPanel extends Panel implements
+ ItemListener
+ {
+ private AnnotationColumnChooser aColChooser;
+
+ private Choice furtherAction = new Choice();
+
+ public FurtherActionPanel(AnnotationColumnChooser aColChooser)
+ {
+ this.aColChooser = aColChooser;
+ furtherAction.addItem("Select");
+ furtherAction.addItem("Hide");
+ furtherAction.addItemListener(this);
+ syncState();
+
+ // this.setTitle("Filter Actions");
+ // this.setFont(JvSwingUtils.getLabelFont());
+
+ this.add(furtherAction);
+ }
+
+ public void syncState()
+ {
+ if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
+ {
+ furtherAction.select("Hide");
+ }
+ else
+ {
+ furtherAction.select("Select");
+ }
+ }
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ aColChooser.setCurrentFutherActionPanel(this);
+ if (furtherAction.getSelectedItem().equalsIgnoreCase("Select"))
+ {
+ setActionOption(ACTION_OPTION_SELECT);
+ updateView();
+ }
+ else
+ {
+ setActionOption(ACTION_OPTION_HIDE);
+ updateView();
+ }
+
+ }
+ }
+
+ public class StructureFilterPanel extends TitledPanel implements
+ ItemListener
+ {
+ private AnnotationColumnChooser aColChooser;
+
+ private Checkbox alphaHelix = new Checkbox();
+
+ private Checkbox betaStrand = new Checkbox();
+
+ private Checkbox turn = new Checkbox();
+
+ private Checkbox all = new Checkbox();
+
+ public StructureFilterPanel(AnnotationColumnChooser aColChooser)
+ {
+ this.aColChooser = aColChooser;
+
+ alphaHelix.setLabel(MessageManager.getString("label.alpha_helix"));
+ alphaHelix.setBackground(Color.white);
+
+ alphaHelix.addItemListener(this);
+
+ betaStrand.setLabel(MessageManager.getString("label.beta_strand"));
+ betaStrand.setBackground(Color.white);
+ betaStrand.addItemListener(this);
+
+ turn.setLabel(MessageManager.getString("label.turn"));
+ turn.setBackground(Color.white);
+ turn.addItemListener(this);
+
+ all.setLabel(MessageManager.getString("label.select_all"));
+ all.setBackground(Color.white);
+ all.addItemListener(this);
+
+ this.setBackground(Color.white);
+ this.setTitle("Structure Filter");
+ this.setFont(JvSwingUtils.getLabelFont());
+
+ this.add(all);
+ this.add(alphaHelix);
+ this.add(betaStrand);
+ this.add(turn);
+ }
+
+ public void alphaHelix_actionPerformed()
+ {
+ updateSelectAllState();
+ aColChooser.setCurrentStructureFilterPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void betaStrand_actionPerformed()
+ {
+ updateSelectAllState();
+ aColChooser.setCurrentStructureFilterPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void turn_actionPerformed()
+ {
+ updateSelectAllState();
+ aColChooser.setCurrentStructureFilterPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void all_actionPerformed()
+ {
+ if (all.getState())
+ {
+ alphaHelix.setState(true);
+ betaStrand.setState(true);
+ turn.setState(true);
+ }
+ else
+ {
+ alphaHelix.setState(false);
+ betaStrand.setState(false);
+ turn.setState(false);
+ }
+ aColChooser.setCurrentStructureFilterPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void updateSelectAllState()
+ {
+ if (alphaHelix.getState() && betaStrand.getState() && turn.getState())
+ {
+ all.setState(true);
+ }
+ else
+ {
+ all.setState(false);
+ }
+ }
+
+ public void syncState()
+ {
+ StructureFilterPanel sfp = aColChooser
+ .getCurrentStructureFilterPanel();
+ if (sfp != null)
+ {
+ alphaHelix.setState(sfp.alphaHelix.getState());
+ betaStrand.setState(sfp.betaStrand.getState());
+ turn.setState(sfp.turn.getState());
+ if (sfp.all.getState())
+ {
+ all.setState(true);
+ alphaHelix.setState(true);
+ betaStrand.setState(true);
+ turn.setState(true);
+ }
+ }
+
+ }
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (e.getSource() == alphaHelix)
+ {
+ alphaHelix_actionPerformed();
+ }
+ else if (e.getSource() == betaStrand)
+ {
+ betaStrand_actionPerformed();
+ }
+ else if (e.getSource() == turn)
+ {
+ turn_actionPerformed();
+ }
+ else if (e.getSource() == all)
+ {
+ all_actionPerformed();
+ }
+ }
+ }
+
+ public class SearchPanel extends TitledPanel implements ItemListener
+ {
+ private AnnotationColumnChooser aColChooser;
+
+ private Checkbox displayName = new Checkbox();
+
+ private Checkbox description = new Checkbox();
+
+ private TextField searchBox = new TextField(10);
+
+ public SearchPanel(AnnotationColumnChooser aColChooser)
+ {
+
+ this.aColChooser = aColChooser;
+ searchBox.addTextListener(new TextListener()
+ {
+
+ @Override
+ public void textValueChanged(TextEvent e)
+ {
+ searchStringAction();
+
+ }
+
+ });
+
+ displayName.setLabel(MessageManager.getString("label.display_name"));
+ displayName.setEnabled(false);
+ displayName.addItemListener(this);
+
+ description.setLabel(MessageManager.getString("label.description"));
+ description.setEnabled(false);
+ description.addItemListener(this);
+ this.setTitle("Search Filter");
+ this.setFont(JvSwingUtils.getLabelFont());
+
+ syncState();
+ this.add(searchBox);
+ this.add(displayName);
+ this.add(description);
+ }
+
+ public void displayNameCheckboxAction()
+ {
+ aColChooser.setCurrentSearchPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void discriptionCheckboxAction()
+ {
+ aColChooser.setCurrentSearchPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void searchStringAction()
+ {
+ aColChooser.setCurrentSearchPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void syncState()
+ {
+ SearchPanel sp = aColChooser.getCurrentSearchPanel();
+ if (sp != null)
+ {
+ description.setEnabled(sp.description.isEnabled());
+ description.setState(sp.description.getState());
+
+ displayName.setEnabled(sp.displayName.isEnabled());
+ displayName.setState(sp.displayName.getState());
+
+ searchBox.setText(sp.searchBox.getText());
+ }
+ }
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (e.getSource() == displayName)
+ {
+ displayNameCheckboxAction();
+ }
+ else if (e.getSource() == description)
+ {
+ discriptionCheckboxAction();
+ }
+
+ }
+ }
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ if (evt.getSource() == thresholdValue)
+ {
+ try
+ {
+ float f = new Float(thresholdValue.getText()).floatValue();
+ slider.setValue((int) (f * 1000));
+ adjustmentValueChanged(null);
+ } catch (NumberFormatException ex)
+ {
+ }
+ }
+
+ else if (evt.getSource() == ok)
+ {
+ ok_actionPerformed(null);
+ }
+ else if (evt.getSource() == cancel)
+ {
+ cancel_actionPerformed(null);
+ }
+ else if (evt.getSource() == thresholdValue)
+ {
+ thresholdValue_actionPerformed(null);
+ }
+ else
+ {
+ updateView();
+ }
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ if (e.getSource() == slider)
+ {
+ updateView();
+ }
+
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent e)
+ {
+ if (e.getSource() == slider)
+ {
+ updateView();
+ }
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ if (e.getSource() == slider)
+ {
+ updateView();
+ }
+ }
+
+ @Override
+ public void mouseExited(MouseEvent e)
+ {
+ if (e.getSource() == slider)
+ {
+ updateView();
+ }
+ }
+
+}
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
- *
- * 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 <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.appletgui;
-
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-
-import java.awt.Color;
-import java.awt.FontMetrics;
-import java.awt.Graphics;
-import java.awt.Image;
-import java.awt.Panel;
-
-public class SeqCanvas extends Panel
-{
- FeatureRenderer fr;
-
- SequenceRenderer sr;
-
- Image img;
-
- Graphics gg;
-
- int imgWidth;
-
- int imgHeight;
-
- AlignViewport av;
-
- SearchResults searchResults = null;
-
- boolean fastPaint = false;
-
- int cursorX = 0;
-
- int cursorY = 0;
-
- public SeqCanvas(AlignViewport av)
- {
- this.av = av;
- fr = new FeatureRenderer(av);
- sr = new SequenceRenderer(av);
- PaintRefresher.Register(this, av.getSequenceSetId());
- }
-
- public AlignViewport getViewport()
- {
- return av;
- }
-
- public FeatureRenderer getFeatureRenderer()
- {
- return fr;
- }
-
- public SequenceRenderer getSequenceRenderer()
- {
- return sr;
- }
-
- void drawNorthScale(Graphics g, int startx, int endx, int ypos)
- {
- int scalestartx = startx - startx % 10 + 10;
-
- g.setColor(Color.black);
-
- // NORTH SCALE
- for (int i = scalestartx; i < endx; i += 10)
- {
- int value = i;
- if (av.hasHiddenColumns())
- {
- value = av.getColumnSelection().adjustForHiddenColumns(value);
- }
-
- g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,
- ypos - (av.charHeight / 2));
-
- g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
- (ypos + 2) - (av.charHeight / 2),
- ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
- ypos - 2);
- }
- }
-
- void drawWestScale(Graphics g, int startx, int endx, int ypos)
- {
- FontMetrics fm = getFontMetrics(av.getFont());
- ypos += av.charHeight;
- if (av.hasHiddenColumns())
- {
- startx = av.getColumnSelection().adjustForHiddenColumns(startx);
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);
- }
-
- int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
- }
-
- // WEST SCALE
- for (int i = 0; i < av.getAlignment().getHeight(); i++)
- {
- SequenceI seq = av.getAlignment().getSequenceAt(i);
- int index = startx;
- int value = -1;
-
- while (index < endx)
- {
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
- {
- index++;
-
- continue;
- }
-
- value = av.getAlignment().getSequenceAt(i).findPosition(index);
-
- break;
- }
-
- if (value != -1)
- {
- int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
- - av.charWidth / 2;
- g.drawString(value + "", x, (ypos + (i * av.charHeight))
- - (av.charHeight / 5));
- }
- }
- }
-
- void drawEastScale(Graphics g, int startx, int endx, int ypos)
- {
- ypos += av.charHeight;
-
- if (av.hasHiddenColumns())
- {
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);
- }
-
- SequenceI seq;
- // EAST SCALE
- for (int i = 0; i < av.getAlignment().getHeight(); i++)
- {
- seq = av.getAlignment().getSequenceAt(i);
- int index = endx;
- int value = -1;
-
- while (index > startx)
- {
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
- {
- index--;
-
- continue;
- }
-
- value = seq.findPosition(index);
-
- break;
- }
-
- if (value != -1)
- {
- g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight))
- - (av.charHeight / 5));
- }
- }
- }
-
- int lastsr = 0;
-
- void fastPaint(int horizontal, int vertical)
- {
- if (fastPaint || gg == null)
- {
- return;
- }
-
- // Its possible on certain browsers that the call to fastpaint
- // is faster than it can paint, so this check here catches
- // this possibility
- if (lastsr + horizontal != av.startRes)
- {
- horizontal = av.startRes - lastsr;
- }
-
- lastsr = av.startRes;
-
- fastPaint = true;
- gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight,
- imgWidth - horizontal * av.charWidth, imgHeight - vertical
- * av.charHeight, -horizontal * av.charWidth, -vertical
- * av.charHeight);
-
- int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;
-
- if (horizontal > 0) // scrollbar pulled right, image to the left
- {
- transX = (er - sr - horizontal) * av.charWidth;
- sr = er - horizontal;
- }
- else if (horizontal < 0)
- {
- er = sr - horizontal;
- }
-
- else if (vertical > 0) // scroll down
- {
- ss = es - vertical;
- if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
- {
- ss = av.startSeq;
- }
- else
- {
- transY = imgHeight - vertical * av.charHeight;
- }
- }
- else if (vertical < 0)
- {
- es = ss - vertical;
- if (es > av.endSeq)
- {
- es = av.endSeq;
- }
- }
-
- gg.translate(transX, transY);
-
- drawPanel(gg, sr, er, ss, es, 0);
- gg.translate(-transX, -transY);
-
- repaint();
-
- }
-
- /**
- * Definitions of startx and endx (hopefully): SMJS This is what I'm working
- * towards! startx is the first residue (starting at 0) to display. endx is
- * the last residue to display (starting at 0). starty is the first sequence
- * to display (starting at 0). endy is the last sequence to display (starting
- * at 0). NOTE 1: The av limits are set in setFont in this class and in the
- * adjustment listener in SeqPanel when the scrollbars move.
- */
- public void update(Graphics g)
- {
- paint(g);
- }
-
- public void paint(Graphics g)
- {
-
- if (img != null
- && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g
- .getClipBounds().height)))
- {
- g.drawImage(img, 0, 0, this);
- fastPaint = false;
- return;
- }
-
- if (fastPaint)
- {
- g.drawImage(img, 0, 0, this);
- fastPaint = false;
- return;
- }
-
- // this draws the whole of the alignment
- imgWidth = this.getSize().width;
- imgHeight = this.getSize().height;
-
- imgWidth -= imgWidth % av.charWidth;
- imgHeight -= imgHeight % av.charHeight;
-
- if (imgWidth < 1 || imgHeight < 1)
- {
- return;
- }
-
- if (img == null || imgWidth != img.getWidth(this)
- || imgHeight != img.getHeight(this))
- {
- img = createImage(imgWidth, imgHeight);
- gg = img.getGraphics();
- gg.setFont(av.getFont());
- }
-
- gg.setColor(Color.white);
- gg.fillRect(0, 0, imgWidth, imgHeight);
-
- if (av.getWrapAlignment())
- {
- drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
- }
- else
- {
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
- }
-
- g.drawImage(img, 0, 0, this);
-
- }
-
- int LABEL_WEST, LABEL_EAST;
-
- public int getWrappedCanvasWidth(int cwidth)
- {
- cwidth -= cwidth % av.charWidth;
-
- FontMetrics fm = getFontMetrics(av.getFont());
-
- LABEL_EAST = 0;
- LABEL_WEST = 0;
-
- if (av.scaleRightWrapped)
- {
- LABEL_EAST = fm.stringWidth(getMask());
- }
-
- if (av.scaleLeftWrapped)
- {
- LABEL_WEST = fm.stringWidth(getMask());
- }
-
- return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
- }
-
- /**
- * Generates a string of zeroes.
- *
- * @return String
- */
- String getMask()
- {
- String mask = "0";
- int maxWidth = 0;
- int tmp;
- AlignmentI alignment = av.getAlignment();
- for (int i = 0; i < alignment.getHeight(); i++)
- {
- tmp = alignment.getSequenceAt(i).getEnd();
- if (tmp > maxWidth)
- {
- maxWidth = tmp;
- }
- }
-
- for (int i = maxWidth; i > 0; i /= 10)
- {
- mask += "0";
- }
- return mask;
- }
-
- public void drawWrappedPanel(Graphics g, int canvasWidth,
- int canvasHeight, int startRes)
- {
- AlignmentI al = av.getAlignment();
-
- FontMetrics fm = getFontMetrics(av.getFont());
-
- if (av.scaleRightWrapped)
- {
- LABEL_EAST = fm.stringWidth(getMask());
- }
-
- if (av.scaleLeftWrapped)
- {
- LABEL_WEST = fm.stringWidth(getMask());
- }
-
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
- {
- hgap += av.charHeight;
- }
-
- int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
- int cHeight = av.getAlignment().getHeight() * av.charHeight;
-
- av.setWrappedWidth(cWidth);
-
- av.endRes = av.startRes + cWidth;
-
- int endx;
- int ypos = hgap;
-
- int maxwidth = av.getAlignment().getWidth() - 1;
-
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
- }
-
- while ((ypos <= canvasHeight) && (startRes < maxwidth))
- {
- endx = startRes + cWidth - 1;
-
- if (endx > maxwidth)
- {
- endx = maxwidth;
- }
-
- g.setColor(Color.black);
-
- if (av.scaleLeftWrapped)
- {
- drawWestScale(g, startRes, endx, ypos);
- }
-
- if (av.scaleRightWrapped)
- {
- g.translate(canvasWidth - LABEL_EAST, 0);
- drawEastScale(g, startRes, endx, ypos);
- g.translate(-(canvasWidth - LABEL_EAST), 0);
- }
-
- g.translate(LABEL_WEST, 0);
-
- if (av.scaleAboveWrapped)
- {
- drawNorthScale(g, startRes, endx, ypos);
- }
- if (av.hasHiddenColumns() && av.showHiddenMarkers)
- {
- g.setColor(Color.blue);
- int res;
- for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
- .size(); i++)
- {
- res = av.getColumnSelection().findHiddenRegionPosition(i)
- - startRes;
-
- if (res < 0 || res > endx - startRes)
- {
- continue;
- }
-
- gg.fillPolygon(new int[]
- { res * av.charWidth - av.charHeight / 4,
- res * av.charWidth + av.charHeight / 4, res * av.charWidth },
- new int[]
- { ypos - (av.charHeight / 2), ypos - (av.charHeight / 2),
- ypos - (av.charHeight / 2) + 8 }, 3);
-
- }
- }
-
- if (g.getClip() == null)
- {
- g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
- }
-
- drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
- g.setClip(null);
-
- if (av.showAnnotation)
- {
- g.translate(0, cHeight + ypos + 4);
- if (annotations == null)
- {
- annotations = new AnnotationPanel(av);
- }
-
- annotations.drawComponent(g, startRes, endx + 1);
- g.translate(0, -cHeight - ypos - 4);
- }
- g.translate(-LABEL_WEST, 0);
-
- ypos += cHeight + getAnnotationHeight() + hgap;
-
- startRes += cWidth;
- }
-
- }
-
- AnnotationPanel annotations;
-
- int getAnnotationHeight()
- {
- if (!av.showAnnotation)
- {
- return 0;
- }
-
- if (annotations == null)
- {
- annotations = new AnnotationPanel(av);
- }
-
- return annotations.adjustPanelHeight();
- }
-
- void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
- int endSeq, int offset)
- {
- if (!av.hasHiddenColumns())
- {
- draw(g1, startRes, endRes, startSeq, endSeq, offset);
- }
- else
- {
- java.util.List<int[]> regions = av.getColumnSelection()
- .getHiddenColumns();
-
- int screenY = 0;
- int blockStart = startRes;
- int blockEnd = endRes;
-
- for (int i = 0; i < regions.size(); i++)
- {
- int[] region = regions.get(i);
- int hideStart = region[0];
- int hideEnd = region[1];
-
- if (hideStart <= blockStart)
- {
- blockStart += (hideEnd - hideStart) + 1;
- continue;
- }
-
- blockEnd = hideStart - 1;
-
- g1.translate(screenY * av.charWidth, 0);
-
- draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
-
- if (av.getShowHiddenMarkers())
- {
- g1.setColor(Color.blue);
- g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1,
- 0 + offset, (blockEnd - blockStart + 1) * av.charWidth
- - 1, (endSeq - startSeq) * av.charHeight + offset);
- }
-
- g1.translate(-screenY * av.charWidth, 0);
- screenY += blockEnd - blockStart + 1;
- blockStart = hideEnd + 1;
- }
-
- if (screenY <= (endRes - startRes))
- {
- blockEnd = blockStart + (endRes - startRes) - screenY;
- g1.translate(screenY * av.charWidth, 0);
- draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
-
- g1.translate(-screenY * av.charWidth, 0);
- }
- }
-
- }
-
- // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
- // int x1, int x2, int y1, int y2, int startx, int starty,
- void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,
- int offset)
- {
- g.setFont(av.getFont());
- sr.prepare(g, av.renderGaps);
-
- SequenceI nextSeq;
-
- // / First draw the sequences
- // ///////////////////////////
- for (int i = startSeq; i < endSeq; i++)
- {
- nextSeq = av.getAlignment().getSequenceAt(i);
-
- if (nextSeq == null)
- {
- continue;
- }
-
- sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
- startRes, endRes, offset + ((i - startSeq) * av.charHeight));
-
- if (av.isShowSequenceFeatures())
- {
- fr.drawSequence(g, nextSeq, startRes, endRes, offset
- + ((i - startSeq) * av.charHeight));
- }
-
- // / Highlight search Results once all sequences have been drawn
- // ////////////////////////////////////////////////////////
- if (searchResults != null)
- {
- int[] visibleResults = searchResults.getResults(nextSeq, startRes,
- endRes);
- if (visibleResults != null)
- {
- for (int r = 0; r < visibleResults.length; r += 2)
- {
- sr.drawHighlightedText(nextSeq, visibleResults[r],
- visibleResults[r + 1], (visibleResults[r] - startRes)
- * av.charWidth, offset
- + ((i - startSeq) * av.charHeight));
- }
- }
- }
-
- if (av.cursorMode && cursorY == i && cursorX >= startRes
- && cursorX <= endRes)
- {
- sr.drawCursor(nextSeq, cursorX,
- (cursorX - startRes) * av.charWidth, offset
- + ((i - startSeq) * av.charHeight));
- }
- }
-
- if (av.getSelectionGroup() != null
- || av.getAlignment().getGroups().size() > 0)
- {
- drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
- }
-
- }
-
- void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
- int startSeq, int endSeq, int offset)
- {
- //
- // ///////////////////////////////////
- // Now outline any areas if necessary
- // ///////////////////////////////////
- SequenceGroup group = av.getSelectionGroup();
-
- int sx = -1;
- int sy = -1;
- int ex = -1;
- int groupIndex = -1;
-
- if ((group == null) && (av.getAlignment().getGroups().size() > 0))
- {
- group = av.getAlignment().getGroups().get(0);
- groupIndex = 0;
- }
-
- if (group != null)
- {
- do
- {
- int oldY = -1;
- int i = 0;
- boolean inGroup = false;
- int top = -1;
- int bottom = -1;
- int alHeight = av.getAlignment().getHeight() - 1;
-
- for (i = startSeq; i < endSeq; i++)
- {
- sx = (group.getStartRes() - startRes) * av.charWidth;
- sy = offset + ((i - startSeq) * av.charHeight);
- ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1;
-
- if (sx + ex < 0 || sx > imgWidth)
- {
- continue;
- }
-
- if ((sx <= (endRes - startRes) * av.charWidth)
- && group.getSequences(null).contains(
- av.getAlignment().getSequenceAt(i)))
- {
- if ((bottom == -1)
- && (i >= alHeight || !group.getSequences(null)
- .contains(
- av.getAlignment().getSequenceAt(i + 1))))
- {
- bottom = sy + av.charHeight;
- }
-
- if (!inGroup)
- {
- if (((top == -1) && (i == 0))
- || !group.getSequences(null).contains(
- av.getAlignment().getSequenceAt(i - 1)))
- {
- top = sy;
- }
-
- oldY = sy;
- inGroup = true;
-
- if (group == av.getSelectionGroup())
- {
- g.setColor(Color.red);
- }
- else
- {
- g.setColor(group.getOutlineColour());
- }
- }
- }
- else
- {
- if (inGroup)
- {
- if (sx >= 0 && sx < imgWidth)
- {
- g.drawLine(sx, oldY, sx, sy);
- }
-
- if (sx + ex < imgWidth)
- {
- g.drawLine(sx + ex, oldY, sx + ex, sy);
- }
-
- if (sx < 0)
- {
- ex += sx;
- sx = 0;
- }
-
- if (sx + ex > imgWidth)
- {
- ex = imgWidth;
- }
-
- else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
- {
- ex = (endRes - startRes + 1) * av.charWidth;
- }
-
- if (top != -1)
- {
- g.drawLine(sx, top, sx + ex, top);
- top = -1;
- }
-
- if (bottom != -1)
- {
- g.drawLine(sx, bottom, sx + ex, bottom);
- bottom = -1;
- }
-
- inGroup = false;
- }
- }
- }
-
- if (inGroup)
- {
- sy = offset + ((i - startSeq) * av.charHeight);
- if (sx >= 0 && sx < imgWidth)
- {
- g.drawLine(sx, oldY, sx, sy);
- }
-
- if (sx + ex < imgWidth)
- {
- g.drawLine(sx + ex, oldY, sx + ex, sy);
- }
-
- if (sx < 0)
- {
- ex += sx;
- sx = 0;
- }
-
- if (sx + ex > imgWidth)
- {
- ex = imgWidth;
- }
- else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
- {
- ex = (endRes - startRes + 1) * av.charWidth;
- }
-
- if (top != -1)
- {
- g.drawLine(sx, top, sx + ex, top);
- top = -1;
- }
-
- if (bottom != -1)
- {
- g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
- bottom = -1;
- }
-
- inGroup = false;
- }
-
- groupIndex++;
-
- if (groupIndex >= av.getAlignment().getGroups().size())
- {
- break;
- }
-
- group = av.getAlignment().getGroups()
- .get(groupIndex);
- } while (groupIndex < av.getAlignment().getGroups().size());
-
- }
- }
-
- public void highlightSearchResults(SearchResults results)
- {
- searchResults = results;
-
- repaint();
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)\r
+ * Copyright (C) 2014 The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview 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 3\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+ */\r
+package jalview.appletgui;\r
+\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.SearchResults;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.datamodel.SequenceI;\r
+\r
+import java.awt.Color;\r
+import java.awt.FontMetrics;\r
+import java.awt.Graphics;\r
+import java.awt.Image;\r
+import java.awt.Panel;\r
+\r
+public class SeqCanvas extends Panel\r
+{\r
+ FeatureRenderer fr;\r
+\r
+ SequenceRenderer sr;\r
+\r
+ Image img;\r
+\r
+ Graphics gg;\r
+\r
+ int imgWidth;\r
+\r
+ int imgHeight;\r
+\r
+ AlignViewport av;\r
+\r
+ SearchResults searchResults = null;\r
+\r
+ boolean fastPaint = false;\r
+\r
+ int cursorX = 0;\r
+\r
+ int cursorY = 0;\r
+\r
+ public SeqCanvas(AlignViewport av)\r
+ {\r
+ this.av = av;\r
+ fr = new FeatureRenderer(av);\r
+ sr = new SequenceRenderer(av);\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
+ }\r
+\r
+ public AlignViewport getViewport()\r
+ {\r
+ return av;\r
+ }\r
+\r
+ public FeatureRenderer getFeatureRenderer()\r
+ {\r
+ return fr;\r
+ }\r
+\r
+ public SequenceRenderer getSequenceRenderer()\r
+ {\r
+ return sr;\r
+ }\r
+\r
+ void drawNorthScale(Graphics g, int startx, int endx, int ypos)\r
+ {\r
+ int scalestartx = startx - startx % 10 + 10;\r
+\r
+ g.setColor(Color.black);\r
+\r
+ // NORTH SCALE\r
+ for (int i = scalestartx; i < endx; i += 10)\r
+ {\r
+ int value = i;\r
+ if (av.hasHiddenColumns())\r
+ {\r
+ value = av.getColumnSelection().adjustForHiddenColumns(value);\r
+ }\r
+\r
+ g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,\r
+ ypos - (av.charHeight / 2));\r
+\r
+ g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),\r
+ (ypos + 2) - (av.charHeight / 2),\r
+ ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),\r
+ ypos - 2);\r
+ }\r
+ }\r
+\r
+ void drawWestScale(Graphics g, int startx, int endx, int ypos)\r
+ {\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+ ypos += av.charHeight;\r
+ if (av.hasHiddenColumns())\r
+ {\r
+ startx = av.getColumnSelection().adjustForHiddenColumns(startx);\r
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
+ }\r
+\r
+ int maxwidth = av.getAlignment().getWidth();\r
+ if (av.hasHiddenColumns())\r
+ {\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+ }\r
+\r
+ // WEST SCALE\r
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
+ {\r
+ SequenceI seq = av.getAlignment().getSequenceAt(i);\r
+ int index = startx;\r
+ int value = -1;\r
+\r
+ while (index < endx)\r
+ {\r
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
+ {\r
+ index++;\r
+\r
+ continue;\r
+ }\r
+\r
+ value = av.getAlignment().getSequenceAt(i).findPosition(index);\r
+\r
+ break;\r
+ }\r
+\r
+ if (value != -1)\r
+ {\r
+ int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))\r
+ - av.charWidth / 2;\r
+ g.drawString(value + "", x, (ypos + (i * av.charHeight))\r
+ - (av.charHeight / 5));\r
+ }\r
+ }\r
+ }\r
+\r
+ void drawEastScale(Graphics g, int startx, int endx, int ypos)\r
+ {\r
+ ypos += av.charHeight;\r
+\r
+ if (av.hasHiddenColumns())\r
+ {\r
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
+ }\r
+\r
+ SequenceI seq;\r
+ // EAST SCALE\r
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
+ {\r
+ seq = av.getAlignment().getSequenceAt(i);\r
+ int index = endx;\r
+ int value = -1;\r
+\r
+ while (index > startx)\r
+ {\r
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
+ {\r
+ index--;\r
+\r
+ continue;\r
+ }\r
+\r
+ value = seq.findPosition(index);\r
+\r
+ break;\r
+ }\r
+\r
+ if (value != -1)\r
+ {\r
+ g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight))\r
+ - (av.charHeight / 5));\r
+ }\r
+ }\r
+ }\r
+\r
+ int lastsr = 0;\r
+\r
+ void fastPaint(int horizontal, int vertical)\r
+ {\r
+ if (fastPaint || gg == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ // Its possible on certain browsers that the call to fastpaint\r
+ // is faster than it can paint, so this check here catches\r
+ // this possibility\r
+ if (lastsr + horizontal != av.startRes)\r
+ {\r
+ horizontal = av.startRes - lastsr;\r
+ }\r
+\r
+ lastsr = av.startRes;\r
+\r
+ fastPaint = true;\r
+ gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight,\r
+ imgWidth - horizontal * av.charWidth, imgHeight - vertical\r
+ * av.charHeight, -horizontal * av.charWidth, -vertical\r
+ * av.charHeight);\r
+\r
+ int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;\r
+\r
+ if (horizontal > 0) // scrollbar pulled right, image to the left\r
+ {\r
+ transX = (er - sr - horizontal) * av.charWidth;\r
+ sr = er - horizontal;\r
+ }\r
+ else if (horizontal < 0)\r
+ {\r
+ er = sr - horizontal;\r
+ }\r
+\r
+ else if (vertical > 0) // scroll down\r
+ {\r
+ ss = es - vertical;\r
+ if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time\r
+ {\r
+ ss = av.startSeq;\r
+ }\r
+ else\r
+ {\r
+ transY = imgHeight - vertical * av.charHeight;\r
+ }\r
+ }\r
+ else if (vertical < 0)\r
+ {\r
+ es = ss - vertical;\r
+ if (es > av.endSeq)\r
+ {\r
+ es = av.endSeq;\r
+ }\r
+ }\r
+\r
+ gg.translate(transX, transY);\r
+\r
+ drawPanel(gg, sr, er, ss, es, 0);\r
+ gg.translate(-transX, -transY);\r
+\r
+ repaint();\r
+\r
+ }\r
+\r
+ /**\r
+ * Definitions of startx and endx (hopefully): SMJS This is what I'm working\r
+ * towards! startx is the first residue (starting at 0) to display. endx is\r
+ * the last residue to display (starting at 0). starty is the first sequence\r
+ * to display (starting at 0). endy is the last sequence to display (starting\r
+ * at 0). NOTE 1: The av limits are set in setFont in this class and in the\r
+ * adjustment listener in SeqPanel when the scrollbars move.\r
+ */\r
+ public void update(Graphics g)\r
+ {\r
+ paint(g);\r
+ }\r
+\r
+ public void paint(Graphics g)\r
+ {\r
+\r
+ if (img != null\r
+ && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g\r
+ .getClipBounds().height)))\r
+ {\r
+ g.drawImage(img, 0, 0, this);\r
+ fastPaint = false;\r
+ return;\r
+ }\r
+\r
+ if (fastPaint)\r
+ {\r
+ g.drawImage(img, 0, 0, this);\r
+ fastPaint = false;\r
+ return;\r
+ }\r
+\r
+ // this draws the whole of the alignment\r
+ imgWidth = this.getSize().width;\r
+ imgHeight = this.getSize().height;\r
+\r
+ imgWidth -= imgWidth % av.charWidth;\r
+ imgHeight -= imgHeight % av.charHeight;\r
+\r
+ if (imgWidth < 1 || imgHeight < 1)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (img == null || imgWidth != img.getWidth(this)\r
+ || imgHeight != img.getHeight(this))\r
+ {\r
+ img = createImage(imgWidth, imgHeight);\r
+ gg = img.getGraphics();\r
+ gg.setFont(av.getFont());\r
+ }\r
+\r
+ gg.setColor(Color.white);\r
+ gg.fillRect(0, 0, imgWidth, imgHeight);\r
+\r
+ if (av.getWrapAlignment())\r
+ {\r
+ drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);\r
+ }\r
+ else\r
+ {\r
+ drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);\r
+ }\r
+\r
+ g.drawImage(img, 0, 0, this);\r
+\r
+ }\r
+\r
+ int LABEL_WEST, LABEL_EAST;\r
+\r
+ public int getWrappedCanvasWidth(int cwidth)\r
+ {\r
+ cwidth -= cwidth % av.charWidth;\r
+\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+\r
+ LABEL_EAST = 0;\r
+ LABEL_WEST = 0;\r
+\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ LABEL_EAST = fm.stringWidth(getMask());\r
+ }\r
+\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ LABEL_WEST = fm.stringWidth(getMask());\r
+ }\r
+\r
+ return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
+ }\r
+\r
+ /**\r
+ * Generates a string of zeroes.\r
+ * \r
+ * @return String\r
+ */\r
+ String getMask()\r
+ {\r
+ String mask = "0";\r
+ int maxWidth = 0;\r
+ int tmp;\r
+ AlignmentI alignment = av.getAlignment();\r
+ for (int i = 0; i < alignment.getHeight(); i++)\r
+ {\r
+ tmp = alignment.getSequenceAt(i).getEnd();\r
+ if (tmp > maxWidth)\r
+ {\r
+ maxWidth = tmp;\r
+ }\r
+ }\r
+\r
+ for (int i = maxWidth; i > 0; i /= 10)\r
+ {\r
+ mask += "0";\r
+ }\r
+ return mask;\r
+ }\r
+\r
+ public void drawWrappedPanel(Graphics g, int canvasWidth,\r
+ int canvasHeight, int startRes)\r
+ {\r
+ AlignmentI al = av.getAlignment();\r
+\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ LABEL_EAST = fm.stringWidth(getMask());\r
+ }\r
+\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ LABEL_WEST = fm.stringWidth(getMask());\r
+ }\r
+\r
+ int hgap = av.charHeight;\r
+ if (av.scaleAboveWrapped)\r
+ {\r
+ hgap += av.charHeight;\r
+ }\r
+\r
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight;\r
+\r
+ av.setWrappedWidth(cWidth);\r
+\r
+ av.endRes = av.startRes + cWidth;\r
+\r
+ int endx;\r
+ int ypos = hgap;\r
+\r
+ int maxwidth = av.getAlignment().getWidth() - 1;\r
+\r
+ if (av.hasHiddenColumns())\r
+ {\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+ }\r
+\r
+ while ((ypos <= canvasHeight) && (startRes < maxwidth))\r
+ {\r
+ endx = startRes + cWidth - 1;\r
+\r
+ if (endx > maxwidth)\r
+ {\r
+ endx = maxwidth;\r
+ }\r
+\r
+ g.setColor(Color.black);\r
+\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ drawWestScale(g, startRes, endx, ypos);\r
+ }\r
+\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ g.translate(canvasWidth - LABEL_EAST, 0);\r
+ drawEastScale(g, startRes, endx, ypos);\r
+ g.translate(-(canvasWidth - LABEL_EAST), 0);\r
+ }\r
+\r
+ g.translate(LABEL_WEST, 0);\r
+\r
+ if (av.scaleAboveWrapped)\r
+ {\r
+ drawNorthScale(g, startRes, endx, ypos);\r
+ }\r
+ if (av.hasHiddenColumns() && av.showHiddenMarkers)\r
+ {\r
+ g.setColor(Color.blue);\r
+ int res;\r
+ for (int i = 0; i < av.getColumnSelection().getHiddenColumns()\r
+ .size(); i++)\r
+ {\r
+ res = av.getColumnSelection().findHiddenRegionPosition(i)\r
+ - startRes;\r
+\r
+ if (res < 0 || res > endx - startRes)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ gg.fillPolygon(new int[]\r
+ { res * av.charWidth - av.charHeight / 4,\r
+ res * av.charWidth + av.charHeight / 4, res * av.charWidth },\r
+ new int[]\r
+ { ypos - (av.charHeight / 2), ypos - (av.charHeight / 2),\r
+ ypos - (av.charHeight / 2) + 8 }, 3);\r
+\r
+ }\r
+ }\r
+\r
+ if (g.getClip() == null)\r
+ {\r
+ g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);\r
+ }\r
+\r
+ drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);\r
+ g.setClip(null);\r
+\r
+ if (av.showAnnotation)\r
+ {\r
+ g.translate(0, cHeight + ypos + 4);\r
+ if (annotations == null)\r
+ {\r
+ annotations = new AnnotationPanel(av);\r
+ }\r
+\r
+ annotations.drawComponent(g, startRes, endx + 1);\r
+ g.translate(0, -cHeight - ypos - 4);\r
+ }\r
+ g.translate(-LABEL_WEST, 0);\r
+\r
+ ypos += cHeight + getAnnotationHeight() + hgap;\r
+\r
+ startRes += cWidth;\r
+ }\r
+\r
+ }\r
+\r
+ AnnotationPanel annotations;\r
+\r
+ int getAnnotationHeight()\r
+ {\r
+ if (!av.showAnnotation)\r
+ {\r
+ return 0;\r
+ }\r
+\r
+ if (annotations == null)\r
+ {\r
+ annotations = new AnnotationPanel(av);\r
+ }\r
+\r
+ return annotations.adjustPanelHeight();\r
+ }\r
+\r
+ void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,\r
+ int endSeq, int offset)\r
+ {\r
+\r
+\r
+ if (!av.hasHiddenColumns())\r
+ {\r
+ draw(g1, startRes, endRes, startSeq, endSeq, offset);\r
+ }\r
+ else\r
+ {\r
+\r
+ int screenY = 0;\r
+ int blockStart = startRes;\r
+ int blockEnd = endRes;\r
+\r
+ if (av.hasHiddenColumns())\r
+ {\r
+ for (int[] region : av.getColumnSelection().getHiddenColumns())\r
+ {\r
+ int hideStart = region[0];\r
+ int hideEnd = region[1];\r
+\r
+ if (hideStart <= blockStart)\r
+ {\r
+ blockStart += (hideEnd - hideStart) + 1;\r
+ continue;\r
+ }\r
+\r
+ blockEnd = hideStart - 1;\r
+\r
+ g1.translate(screenY * av.charWidth, 0);\r
+\r
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
+\r
+ if (av.getShowHiddenMarkers())\r
+ {\r
+ g1.setColor(Color.blue);\r
+ g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1,\r
+ 0 + offset, (blockEnd - blockStart + 1) * av.charWidth\r
+ - 1, (endSeq - startSeq) * av.charHeight\r
+ + offset);\r
+ }\r
+\r
+ g1.translate(-screenY * av.charWidth, 0);\r
+ screenY += blockEnd - blockStart + 1;\r
+ blockStart = hideEnd + 1;\r
+ }\r
+ }\r
+ if (screenY <= (endRes - startRes))\r
+ {\r
+ blockEnd = blockStart + (endRes - startRes) - screenY;\r
+ g1.translate(screenY * av.charWidth, 0);\r
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
+\r
+ g1.translate(-screenY * av.charWidth, 0);\r
+ }\r
+ }\r
+\r
+ }\r
+\r
+ // int startRes, int endRes, int startSeq, int endSeq, int x, int y,\r
+ // int x1, int x2, int y1, int y2, int startx, int starty,\r
+ void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,\r
+ int offset)\r
+ {\r
+ g.setFont(av.getFont());\r
+ sr.prepare(g, av.renderGaps);\r
+\r
+ SequenceI nextSeq;\r
+\r
+ // / First draw the sequences\r
+ // ///////////////////////////\r
+ for (int i = startSeq; i < endSeq; i++)\r
+ {\r
+ nextSeq = av.getAlignment().getSequenceAt(i);\r
+\r
+ if (nextSeq == null)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),\r
+ startRes, endRes, offset + ((i - startSeq) * av.charHeight));\r
+\r
+ if (av.isShowSequenceFeatures())\r
+ {\r
+ fr.drawSequence(g, nextSeq, startRes, endRes, offset\r
+ + ((i - startSeq) * av.charHeight));\r
+ }\r
+\r
+ // / Highlight search Results once all sequences have been drawn\r
+ // ////////////////////////////////////////////////////////\r
+ if (searchResults != null)\r
+ {\r
+ int[] visibleResults = searchResults.getResults(nextSeq, startRes,\r
+ endRes);\r
+ if (visibleResults != null)\r
+ {\r
+ for (int r = 0; r < visibleResults.length; r += 2)\r
+ {\r
+ sr.drawHighlightedText(nextSeq, visibleResults[r],\r
+ visibleResults[r + 1], (visibleResults[r] - startRes)\r
+ * av.charWidth, offset\r
+ + ((i - startSeq) * av.charHeight));\r
+ }\r
+ }\r
+ }\r
+\r
+ if (av.cursorMode && cursorY == i && cursorX >= startRes\r
+ && cursorX <= endRes)\r
+ {\r
+ sr.drawCursor(nextSeq, cursorX,\r
+ (cursorX - startRes) * av.charWidth, offset\r
+ + ((i - startSeq) * av.charHeight));\r
+ }\r
+ }\r
+\r
+ if (av.getSelectionGroup() != null\r
+ || av.getAlignment().getGroups().size() > 0)\r
+ {\r
+ drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);\r
+ }\r
+\r
+ }\r
+\r
+ void drawGroupsBoundaries(Graphics g, int startRes, int endRes,\r
+ int startSeq, int endSeq, int offset)\r
+ {\r
+ //\r
+ // ///////////////////////////////////\r
+ // Now outline any areas if necessary\r
+ // ///////////////////////////////////\r
+ SequenceGroup group = av.getSelectionGroup();\r
+\r
+ int sx = -1;\r
+ int sy = -1;\r
+ int ex = -1;\r
+ int groupIndex = -1;\r
+\r
+ if ((group == null) && (av.getAlignment().getGroups().size() > 0))\r
+ {\r
+ group = av.getAlignment().getGroups().get(0);\r
+ groupIndex = 0;\r
+ }\r
+\r
+ if (group != null)\r
+ {\r
+ do\r
+ {\r
+ int oldY = -1;\r
+ int i = 0;\r
+ boolean inGroup = false;\r
+ int top = -1;\r
+ int bottom = -1;\r
+ int alHeight = av.getAlignment().getHeight() - 1;\r
+\r
+ for (i = startSeq; i < endSeq; i++)\r
+ {\r
+ sx = (group.getStartRes() - startRes) * av.charWidth;\r
+ sy = offset + ((i - startSeq) * av.charHeight);\r
+ ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1;\r
+\r
+ if (sx + ex < 0 || sx > imgWidth)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if ((sx <= (endRes - startRes) * av.charWidth)\r
+ && group.getSequences(null).contains(\r
+ av.getAlignment().getSequenceAt(i)))\r
+ {\r
+ if ((bottom == -1)\r
+ && (i >= alHeight || !group.getSequences(null)\r
+ .contains(\r
+ av.getAlignment().getSequenceAt(i + 1))))\r
+ {\r
+ bottom = sy + av.charHeight;\r
+ }\r
+\r
+ if (!inGroup)\r
+ {\r
+ if (((top == -1) && (i == 0))\r
+ || !group.getSequences(null).contains(\r
+ av.getAlignment().getSequenceAt(i - 1)))\r
+ {\r
+ top = sy;\r
+ }\r
+\r
+ oldY = sy;\r
+ inGroup = true;\r
+\r
+ if (group == av.getSelectionGroup())\r
+ {\r
+ g.setColor(Color.red);\r
+ }\r
+ else\r
+ {\r
+ g.setColor(group.getOutlineColour());\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (inGroup)\r
+ {\r
+ if (sx >= 0 && sx < imgWidth)\r
+ {\r
+ g.drawLine(sx, oldY, sx, sy);\r
+ }\r
+\r
+ if (sx + ex < imgWidth)\r
+ {\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+ }\r
+\r
+ if (sx < 0)\r
+ {\r
+ ex += sx;\r
+ sx = 0;\r
+ }\r
+\r
+ if (sx + ex > imgWidth)\r
+ {\r
+ ex = imgWidth;\r
+ }\r
+\r
+ else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
+ {\r
+ ex = (endRes - startRes + 1) * av.charWidth;\r
+ }\r
+\r
+ if (top != -1)\r
+ {\r
+ g.drawLine(sx, top, sx + ex, top);\r
+ top = -1;\r
+ }\r
+\r
+ if (bottom != -1)\r
+ {\r
+ g.drawLine(sx, bottom, sx + ex, bottom);\r
+ bottom = -1;\r
+ }\r
+\r
+ inGroup = false;\r
+ }\r
+ }\r
+ }\r
+\r
+ if (inGroup)\r
+ {\r
+ sy = offset + ((i - startSeq) * av.charHeight);\r
+ if (sx >= 0 && sx < imgWidth)\r
+ {\r
+ g.drawLine(sx, oldY, sx, sy);\r
+ }\r
+\r
+ if (sx + ex < imgWidth)\r
+ {\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+ }\r
+\r
+ if (sx < 0)\r
+ {\r
+ ex += sx;\r
+ sx = 0;\r
+ }\r
+\r
+ if (sx + ex > imgWidth)\r
+ {\r
+ ex = imgWidth;\r
+ }\r
+ else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
+ {\r
+ ex = (endRes - startRes + 1) * av.charWidth;\r
+ }\r
+\r
+ if (top != -1)\r
+ {\r
+ g.drawLine(sx, top, sx + ex, top);\r
+ top = -1;\r
+ }\r
+\r
+ if (bottom != -1)\r
+ {\r
+ g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
+ bottom = -1;\r
+ }\r
+\r
+ inGroup = false;\r
+ }\r
+\r
+ groupIndex++;\r
+\r
+ if (groupIndex >= av.getAlignment().getGroups().size())\r
+ {\r
+ break;\r
+ }\r
+\r
+ group = av.getAlignment().getGroups()\r
+ .get(groupIndex);\r
+ } while (groupIndex < av.getAlignment().getGroups().size());\r
+\r
+ }\r
+ }\r
+\r
+ public void highlightSearchResults(SearchResults results)\r
+ {\r
+ searchResults = results;\r
+\r
+ repaint();\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalview.git / commitdiff