--- /dev/null
+package jalview.api;
+
+/**
+ * Common methods for jalview.appletgui.AlignFrame and jalview.gui.AlignFrame in
+ * relation to JalviewJS and the JalviewLiteJSApi
+ *
+ * @author hansonr
+ *
+ */
+public interface AlignFrameI
+{
+
+}
--- /dev/null
+package jalview.api;
+
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.NewickFile;
+import jalview.javascript.JSFunctionExec;
+import jalview.javascript.MouseOverStructureListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.VamsasSource;
+
+import java.applet.AppletContext;
+import java.io.IOException;
+import java.net.URL;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import netscape.javascript.JSObject;
+
+public interface JalviewApp
+{
+ public String getParameter(String name);
+
+ public boolean getDefaultParameter(String name, boolean def);
+
+ public URL getDocumentBase();
+
+ public URL getCodeBase();
+
+ public void setAlignPdbStructures(boolean defaultParameter);
+
+ public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
+ String[] chains, DataSourceType protocol);
+
+ public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
+ String[][] chains, String[] protocols);
+
+ public void updateForAnnotations();
+
+ public AlignViewportI getViewport();
+
+ public void setFeatureGroupState(String[] groups, boolean state);
+
+ public boolean parseFeaturesFile(String param, DataSourceType protocol);
+
+ public void newFeatureSettings();
+
+ public boolean loadScoreFile(String sScoreFile) throws IOException;
+
+ public void loadTree(NewickFile fin, String treeFile) throws IOException;
+
+ public Vector<Runnable> getJsExecQueue(JSFunctionExec jsFunctionExec);
+
+ public AppletContext getAppletContext();
+
+ public boolean isJsfallbackEnabled();
+
+ public JSObject getJSObject();
+
+ public StructureSelectionManagerProvider getStructureSelectionManagerProvider();
+
+ public void updateColoursFromMouseOver(Object source,
+ MouseOverStructureListener mouseOverStructureListener);
+
+ public Object[] getSelectionForListener(SequenceGroup seqsel, ColumnSelection colsel,
+ HiddenColumns hidden, SelectionSource source, Object alignFrame);
+
+ public String arrayToSeparatorList(String[] array);
+
+ public Hashtable<String, int[]> getJSHashes();
+
+ Hashtable<String, Hashtable<String, String[]>> getJSMessages();
+
+ public Object getFrameForSource(VamsasSource source);
+
+ public jalview.renderer.seqfeatures.FeatureRenderer getNewFeatureRenderer(
+ AlignViewportI vp);
+
+}
import jalview.analysis.TreeBuilder;
import jalview.analysis.scoremodels.PIDModel;
import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.AlignFrameI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import org.jmol.viewer.Viewer;
public class AlignFrame extends EmbmenuFrame implements ActionListener,
- ItemListener, KeyListener, AlignViewControllerGuiI
+ ItemListener, KeyListener, AlignViewControllerGuiI, AlignFrameI
{
public AlignViewControllerI avc;
}
else if (source == autoCalculate)
{
- viewport.autoCalculateConsensus = autoCalculate.getState();
+ viewport.setAutoCalculateConsensusAndConservation(autoCalculate.getState());
}
else if (source == sortByTree)
{
import java.awt.event.AdjustmentListener;
import java.awt.event.ComponentAdapter;
import java.awt.event.ComponentEvent;
+import java.awt.image.BufferedImage;
import java.beans.PropertyChangeEvent;
import java.util.List;
return av;
}
+ @Override
public SequenceRenderer getSequenceRenderer()
{
return seqPanel.seqCanvas.sr;
}
+ @Override
+ public void overviewDone(BufferedImage miniMe)
+ {
+ overviewPanel.canvas.finalizeDraw(miniMe);
+ }
+
}
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceGroup;
+import jalview.gui.Preferences;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
private void setDefaultMinMax()
{
minColour.setBackground(av.applet.getDefaultColourParameter(
- "ANNOTATIONCOLOUR_MIN", Color.orange));
+ Preferences.ANNOTATIONCOLOUR_MIN, Color.orange));
maxColour.setBackground(av.applet
- .getDefaultColourParameter("ANNOTATIONCOLOUR_MAX", Color.red));
+ .getDefaultColourParameter(Preferences.ANNOTATIONCOLOUR_MAX, Color.red));
}
{
try
{
- float f = Float.valueOf(thresholdValue.getText()).floatValue();
+ float f = new Float(thresholdValue.getText()).floatValue();
slider.setValue((int) (f * 1000));
adjustmentValueChanged(null);
} catch (NumberFormatException ex)
.getAlignmentAnnotation();
// DETECT RIGHT MOUSE BUTTON IN AWT
- if ((evt.getModifiersEx()
- & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
+ if ((evt.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
PopupMenu popup = new PopupMenu(
}
}
- if ((evt.getModifiersEx()
- & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK
+ if ((evt.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK
&& activeRow != -1)
{
if (av.getColumnSelection() == null
* @author Jim Procter and Andrew Waterhouse
*
*/
-public class EmbmenuFrame extends Frame
- implements MouseListener, AutoCloseable
+@SuppressWarnings("serial")
+public class EmbmenuFrame extends Frame implements MouseListener
{
protected static final Font FONT_ARIAL_PLAIN_11 = new Font("Arial",
Font.PLAIN, 11);
/**
* map from labels to popup menus for the embedded menubar
*/
- protected Map<Label, PopupMenu> embeddedPopup = new HashMap<>();
+ protected Map<Label, PopupMenu> embeddedPopup = new HashMap<Label, PopupMenu>();
/**
* the embedded menu is built on this and should be added to the frame at the
return embeddedMenu;
}
- @Override
public void mousePressed(MouseEvent evt)
{
PopupMenu popup = null;
return embeddedPopup.get(source);
}
- @Override
public void mouseClicked(MouseEvent evt)
{
}
- @Override
public void mouseReleased(MouseEvent evt)
{
}
- @Override
public void mouseEntered(MouseEvent evt)
{
}
- @Override
public void mouseExited(MouseEvent evt)
{
}
/**
* calls destroyMenus()
*/
- @Override
- public void close()
+ public void finalize() throws Throwable
{
destroyMenus();
embeddedPopup = null;
embeddedMenu = null;
+ super.finalize();
}
}
{
try
{
- float f = Float.valueOf(thresholdValue.getText()).floatValue();
+ float f = new Float(thresholdValue.getText()).floatValue();
slider.setValue((int) (f * SCALE_FACTOR_1K));
adjustmentValueChanged(null);
public void mouseClicked(MouseEvent evt)
{
MyCheckbox check = (MyCheckbox) evt.getSource();
- if ((evt.getModifiersEx() & InputEvent.BUTTON3_DOWN_MASK) != 0)
+ if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0)
{
this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY());
}
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Frame;
-import java.awt.GraphicsEnvironment;
import java.awt.Label;
import java.awt.Panel;
+import java.awt.Toolkit;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
*/
void init()
{
- // String fonts[] = Toolkit.getDefaultToolkit().getFontList();
- String fonts[] = GraphicsEnvironment.getLocalGraphicsEnvironment()
- .getAvailableFontFamilyNames();
+ String fonts[] = Toolkit.getDefaultToolkit().getFontList();
for (int i = 0; i < fonts.length; i++)
{
fontName.addItem(fonts[i]);
int seq = alignPanel.seqPanel.findSeq(e);
- if ((e.getModifiersEx()
- & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
+ if ((e.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
SequenceI sq = av.getAlignment().getSequenceAt(seq);
import java.awt.Frame;
import java.awt.Graphics;
import java.awt.Image;
+import java.awt.image.BufferedImage;
+@SuppressWarnings("serial")
public class OverviewCanvas extends Component
{
// This is set true if the alignment view changes whilst
private AlignViewport av;
+ private boolean showSequenceFeatures;
+
+ private boolean showAnnotation;
+
+ private jalview.api.FeatureRenderer featureRenderer;
+
private jalview.renderer.seqfeatures.FeatureRenderer fr;
private Frame nullFrame;
- public OverviewCanvas(OverviewDimensions overviewDims,
+ private OverviewPanel panel;
+
+ public OverviewCanvas(OverviewPanel panel,
+ OverviewDimensions overviewDims,
AlignViewport alignvp)
{
+ this.panel = panel;
od = overviewDims;
av = alignvp;
}
public void draw(boolean showSequenceFeatures, boolean showAnnotation,
- FeatureRenderer transferRenderer)
+ jalview.api.FeatureRenderer featureRenderer)
{
- miniMe = null;
+ this.showSequenceFeatures = showSequenceFeatures;
+ this.showAnnotation = showAnnotation;
+ this.featureRenderer = featureRenderer;
if (showSequenceFeatures)
{
- fr.transferSettings(transferRenderer);
+ fr.transferSettings(featureRenderer);
}
setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
- or = new OverviewRenderer(fr, od, av.getAlignment(),
+ or = new OverviewRenderer(panel.ap, fr, od, av.getAlignment(),
av.getResidueShading(), new OverviewResColourFinder());
- miniMe = nullFrame.createImage(od.getWidth(), od.getHeight());
offscreen = nullFrame.createImage(od.getWidth(), od.getHeight());
-
- miniMe = or.draw(od.getRows(av.getAlignment()),
- od.getColumns(av.getAlignment()));
-
- Graphics mg = miniMe.getGraphics();
-
- // checks for conservation annotation to make sure overview works for DNA
- // too
- if (showAnnotation)
- {
- mg.translate(0, od.getSequencesHeight());
- or.drawGraph(mg, av.getAlignmentConservationAnnotation(),
- od.getGraphHeight(), od.getColumns(av.getAlignment()));
- mg.translate(0, -od.getSequencesHeight());
- }
-
- if (restart)
- {
- restart = false;
- draw(showSequenceFeatures, showAnnotation, transferRenderer);
- }
- else
- {
- updaterunning = false;
- }
+ or.drawMiniMe();
}
@Override
@Override
public void paint(Graphics g)
{
- Graphics og = offscreen.getGraphics();
if (miniMe != null)
{
+ Graphics og = offscreen.getGraphics();
og.drawImage(miniMe, 0, 0, this);
og.setColor(Color.red);
od.drawBox(og);
g.drawImage(offscreen, 0, 0, this);
+ og.dispose();
}
}
od = null;
}
+ public void finalizeDraw(BufferedImage miniMe)
+ {
+ if (restart)
+ {
+ restart = false;
+ draw(showSequenceFeatures, showAnnotation, featureRenderer);
+ }
+ else
+ {
+ this.miniMe = miniMe;
+ // checks for conservation annotation to make sure overview works for DNA
+ // too
+ if (showAnnotation)
+ {
+ or.drawGraph(av.getAlignmentConservationAnnotation());
+ }
+ updaterunning = false;
+ repaint();
+ }
+ }
+
}
import javax.swing.SwingUtilities;
+@SuppressWarnings("serial")
public class OverviewPanel extends Panel implements Runnable,
MouseMotionListener, MouseListener, ViewportListenerI
{
- private OverviewDimensions od;
+ OverviewDimensions od;
- private OverviewCanvas oviewCanvas;
+ OverviewCanvas canvas;
private AlignViewport av;
- private AlignmentPanel ap;
+ AlignmentPanel ap;
private boolean showHidden = true;
(av.isShowAnnotation()
&& av.getSequenceConsensusHash() != null));
- oviewCanvas = new OverviewCanvas(od, av);
+ canvas = new OverviewCanvas(this, od, av);
setLayout(new BorderLayout());
- add(oviewCanvas, BorderLayout.CENTER);
+ add(canvas, BorderLayout.CENTER);
setSize(new Dimension(od.getWidth(), od.getHeight()));
@Override
public void mouseClicked(MouseEvent evt)
{
- if ((evt.getModifiersEx()
- & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
+ if ((evt.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
showPopupMenu(evt);
}
@Override
public void mousePressed(MouseEvent evt)
{
- if ((evt.getModifiersEx()
- & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
+ if ((evt.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
if (!Platform.isMac()) // BH was excluding JavaScript
{
*/
public void updateOverviewImage()
{
- if (oviewCanvas == null)
+ if (canvas == null)
{
/*
* panel has been disposed
{
if (updateRunning)
{
- oviewCanvas.restartDraw();
+ canvas.restartDraw();
return;
}
@Override
public void run()
{
- oviewCanvas.draw(av.isShowSequenceFeatures(),
+ setBoxPosition();
+ canvas.draw(av.isShowSequenceFeatures(),
(av.isShowAnnotation()
&& av.getAlignmentConservationAnnotation() != null),
ap.seqPanel.seqCanvas.getFeatureRenderer());
- setBoxPosition();
}
/**
(av.isShowAnnotation()
&& av.getAlignmentConservationAnnotation() != null));
}
- oviewCanvas.resetOviewDims(od);
+ canvas.resetOviewDims(od);
updateOverviewImage();
}
} finally
{
av = null;
- if (oviewCanvas != null)
+ if (canvas != null)
{
- oviewCanvas.dispose();
+ canvas.dispose();
}
- oviewCanvas = null;
+ canvas = null;
ap = null;
od = null;
}
min = res;
max = res;
- if ((evt.getModifiersEx()
- & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
+ if ((evt.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
rightMouseButtonPressed(evt, res);
}
{ ypos - (avcharHeight / 2), ypos - (avcharHeight / 2), ypos - (avcharHeight / 2) + 8 }, 3);
}
}
-
+ // BH 2020.03.19 avoiding g.setClip at all costs
+ g = g.create();
if (g.getClip() == null)
{
- g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
+ g.clipRect(0, 0, cWidth * avcharWidth, canvasHeight);
}
drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
- g.setClip(null);
+ // g.setClip(null);
+ g.dispose();
if (av.isShowAnnotation())
{
g.translate(0, cHeight + ypos + 4);
import java.awt.event.ItemListener;
public class TreePanel extends EmbmenuFrame
- implements ActionListener, ItemListener, AutoCloseable
+ implements ActionListener, ItemListener
{
SequenceI[] seq;
}
@Override
- public void close()
+ public void finalize() throws Throwable
{
ap = null;
av = null;
- super.close();
+ super.finalize();
}
/**
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.controller;
+
+import jalview.analysis.AlignmentSorter;
+import jalview.api.AlignViewControllerGuiI;
+import jalview.api.AlignViewControllerI;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.commands.OrderCommand;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FeaturesFile;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.util.BitSet;
+import java.util.List;
+
+public class AlignViewController implements AlignViewControllerI
+{
+ AlignViewportI viewport = null;
+
+ AlignmentViewPanel alignPanel = null;
+
+ /**
+ * the GUI container that is handling interactions with the user
+ */
+ private AlignViewControllerGuiI avcg;
+
+ public AlignViewController(AlignViewControllerGuiI alignFrame,
+ AlignViewportI vp, AlignmentViewPanel ap)
+ {
+ this.avcg = alignFrame;
+ this.viewport = vp;
+ this.alignPanel = ap;
+ }
+
+ @Override
+ public void setViewportAndAlignmentPanel(AlignViewportI vp,
+ AlignmentViewPanel ap)
+ {
+ this.alignPanel = ap;
+ this.viewport = vp;
+ }
+
+ @Override
+ public boolean makeGroupsFromSelection()
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ ColumnSelection cs = viewport.getColumnSelection();
+ SequenceGroup[] gps = null;
+ if (sg != null && (cs == null || cs.isEmpty()))
+ {
+ gps = jalview.analysis.Grouping.makeGroupsFrom(
+ viewport.getSequenceSelection(),
+ viewport.getAlignmentView(true)
+ .getSequenceStrings(viewport.getGapCharacter()),
+ viewport.getAlignment().getGroups());
+ }
+ else
+ {
+ if (cs != null)
+ {
+ gps = jalview.analysis.Grouping.makeGroupsFromCols(
+ (sg == null) ? viewport.getAlignment().getSequencesArray()
+ : sg.getSequences().toArray(new SequenceI[0]),
+ cs, viewport.getAlignment().getGroups());
+ }
+ }
+ if (gps != null)
+ {
+ viewport.getAlignment().deleteAllGroups();
+ viewport.clearSequenceColours();
+ viewport.setSelectionGroup(null);
+ ColourSchemeI colours = viewport.getGlobalColourScheme();
+ // set view properties for each group
+ for (int g = 0; g < gps.length; g++)
+ {
+ // gps[g].setShowunconserved(viewport.getShowUnconserved());
+ gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
+ viewport.getAlignment().addGroup(gps[g]);
+ if (colours != null)
+ {
+ gps[g].setColourScheme(colours.getInstance(viewport, gps[g]));
+ }
+ Color col = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
+ gps[g].idColour = col;
+ viewport.setUpdateStructures(true);
+ viewport.addSequenceGroup(gps[g]);
+ }
+ return true;
+ }
+ return false;
+ }
+
+ @Override
+ public boolean createGroup()
+ {
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg != null)
+ {
+ viewport.getAlignment().addGroup(sg);
+ return true;
+ }
+ return false;
+ }
+
+ @Override
+ public boolean unGroup()
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg != null)
+ {
+ viewport.getAlignment().deleteGroup(sg);
+ return true;
+ }
+ return false;
+ }
+
+ @Override
+ public boolean deleteGroups()
+ {
+ if (viewport.getAlignment().getGroups() != null
+ && viewport.getAlignment().getGroups().size() > 0)
+ {
+ viewport.getAlignment().deleteAllGroups();
+ viewport.clearSequenceColours();
+ viewport.setSelectionGroup(null);
+ return true;
+ }
+ return false;
+ }
+
+ @Override
+ public boolean markColumnsContainingFeatures(boolean invert,
+ boolean extendCurrent, boolean toggle, String featureType)
+ {
+ // JBPNote this routine could also mark rows, not just columns.
+ // need a decent query structure to allow all types of feature searches
+ BitSet bs = new BitSet();
+ boolean searchSelection = viewport.getSelectionGroup() != null
+ && !extendCurrent;
+ SequenceCollectionI sqcol = searchSelection ? viewport
+ .getSelectionGroup() : viewport.getAlignment();
+
+ int nseq = findColumnsWithFeature(featureType, sqcol, bs);
+
+ ColumnSelection cs = viewport.getColumnSelection();
+ if (cs == null)
+ {
+ cs = new ColumnSelection();
+ }
+
+ if (bs.cardinality() > 0 || invert)
+ {
+ boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
+ sqcol.getEndRes(), invert, extendCurrent, toggle);
+ if (changed)
+ {
+ viewport.setColumnSelection(cs);
+ alignPanel.paintAlignment(false, false);
+ int columnCount = invert
+ ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+ - bs.cardinality()
+ : bs.cardinality();
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.view_controller_toggled_marked", new String[]
+ { toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked"),
+ String.valueOf(columnCount),
+ invert ? MessageManager
+ .getString("label.not_containing")
+ : MessageManager.getString("label.containing"),
+ featureType, Integer.valueOf(nseq).toString() }));
+ return true;
+ }
+ }
+ else
+ {
+ String key = searchSelection ? "label.no_feature_found_selection"
+ : "label.no_feature_of_type_found";
+ avcg.setStatus(MessageManager.formatMessage(key,
+ new String[] { featureType }));
+ if (!extendCurrent)
+ {
+ cs.clear();
+ alignPanel.paintAlignment(false, false);
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Sets a bit in the BitSet for each column (base 0) in the sequence
+ * collection which includes a visible feature of the specified feature type.
+ * Returns the number of sequences which have the feature visible in the
+ * selected range.
+ *
+ * @param featureType
+ * @param sqcol
+ * @param bs
+ * @return
+ */
+ int findColumnsWithFeature(String featureType,
+ SequenceCollectionI sqcol, BitSet bs)
+ {
+ FeatureRenderer fr = alignPanel == null ? null : alignPanel
+ .getFeatureRenderer();
+
+ final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
+ final int endColumn = sqcol.getEndRes() + 1;
+ List<SequenceI> seqs = sqcol.getSequences();
+ int nseq = 0;
+ for (SequenceI sq : seqs)
+ {
+ if (sq != null)
+ {
+ // int ist = sq.findPosition(sqcol.getStartRes());
+ List<SequenceFeature> sfs = sq.findFeatures(startColumn,
+ endColumn, featureType);
+
+ boolean found = false;
+ for (SequenceFeature sf : sfs)
+ {
+ if (fr.getColour(sf) == null)
+ {
+ continue;
+ }
+ if (!found)
+ {
+ nseq++;
+ }
+ found = true;
+
+ int sfStartCol = sq.findIndex(sf.getBegin());
+ int sfEndCol = sq.findIndex(sf.getEnd());
+
+ if (sf.isContactFeature())
+ {
+ /*
+ * 'contact' feature - check for 'start' or 'end'
+ * position within the selected region
+ */
+ if (sfStartCol >= startColumn && sfStartCol <= endColumn)
+ {
+ bs.set(sfStartCol - 1);
+ }
+ if (sfEndCol >= startColumn && sfEndCol <= endColumn)
+ {
+ bs.set(sfEndCol - 1);
+ }
+ continue;
+ }
+
+ /*
+ * contiguous feature - select feature positions (if any)
+ * within the selected region
+ */
+ if (sfStartCol < startColumn)
+ {
+ sfStartCol = startColumn;
+ }
+ // not sure what the point of this is
+ // if (sfStartCol < ist)
+ // {
+ // sfStartCol = ist;
+ // }
+ if (sfEndCol > endColumn)
+ {
+ sfEndCol = endColumn;
+ }
+ for (; sfStartCol <= sfEndCol; sfStartCol++)
+ {
+ bs.set(sfStartCol - 1); // convert to base 0
+ }
+ }
+ }
+ }
+ return nseq;
+ }
+
+ @Override
+ public void sortAlignmentByFeatureDensity(List<String> typ)
+ {
+ String methodText = MessageManager.getString("label.sort_by_density");
+ sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_DENSITY);
+ }
+
+ /**
+ * Sorts the alignment (or current selection) by either average score or density
+ * of the specified feature types, and adds to the command history. If
+ * {@code types} is null, all visible feature types are used for the sort. If no
+ * feature types apply, does nothing.
+ *
+ * @param types
+ * @param methodText
+ * - text shown in Undo/Redo command
+ * @param method
+ * - passed to
+ * jalview.analysis.AlignmentSorter.sortByFeatures()
+ */
+ protected void sortByFeatures(List<String> types, String methodText,
+ final String method)
+ {
+ FeatureRenderer fr = alignPanel.getFeatureRenderer();
+ if (types == null && fr != null)
+ {
+ types = fr.getDisplayedFeatureTypes();
+ }
+ if (types.isEmpty())
+ {
+ return; // nothing to do
+ }
+ List<String> gps = null;
+ if (fr != null)
+ {
+ gps = fr.getDisplayedFeatureGroups();
+ }
+ AlignmentI al = viewport.getAlignment();
+
+ int start, stop;
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg != null)
+ {
+ start = sg.getStartRes();
+ stop = sg.getEndRes();
+ }
+ else
+ {
+ start = 0;
+ stop = al.getWidth();
+ }
+ SequenceI[] oldOrder = al.getSequencesArray();
+ AlignmentSorter.sortByFeature(types, gps, start, stop, al, method);
+ avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true, false);
+
+ }
+
+ @Override
+ public void sortAlignmentByFeatureScore(List<String> typ)
+ {
+ String methodText = MessageManager.getString("label.sort_by_score");
+ sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_SCORE);
+ }
+
+ @Override
+ public boolean parseFeaturesFile(Object file, DataSourceType protocol,
+ boolean relaxedIdMatching)
+ {
+ boolean featuresAdded = false;
+ FeatureRenderer fr = alignPanel.getFeatureRenderer();
+ try
+ {
+ featuresAdded = new FeaturesFile(false, file, protocol).parse(
+ viewport.getAlignment().getDataset(), fr.getFeatureColours(),
+ fr.getFeatureFilters(), false, relaxedIdMatching);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ if (featuresAdded)
+ {
+ avcg.refreshFeatureUI(true);
+ if (fr != null)
+ {
+ // update the min/max ranges where necessary
+ fr.findAllFeatures(true);
+ }
+ if (avcg.getFeatureSettingsUI() != null)
+ {
+ avcg.getFeatureSettingsUI().discoverAllFeatureData();
+ }
+ alignPanel.paintAlignment(true, true);
+ }
+
+ return featuresAdded;
+
+ }
+
+ @Override
+ public boolean markHighlightedColumns(boolean invert,
+ boolean extendCurrent, boolean toggle)
+ {
+ if (!viewport.hasSearchResults())
+ {
+ // do nothing if no selection exists
+ return false;
+ }
+ // JBPNote this routine could also mark rows, not just columns.
+ BitSet bs = new BitSet();
+ SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
+ || extendCurrent) ? viewport.getAlignment()
+ : viewport.getSelectionGroup();
+
+ // this could be a lambda... - the remains of the method is boilerplate,
+ // except for the different messages for reporting selection.
+ int nseq = viewport.getSearchResults().markColumns(sqcol, bs);
+
+ ColumnSelection cs = viewport.getColumnSelection();
+ if (cs == null)
+ {
+ cs = new ColumnSelection();
+ }
+
+ if (bs.cardinality() > 0 || invert)
+ {
+ boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
+ sqcol.getEndRes(), invert, extendCurrent, toggle);
+ if (changed)
+ {
+ viewport.setColumnSelection(cs);
+ alignPanel.paintAlignment(false, false);
+ int columnCount = invert
+ ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+ - bs.cardinality()
+ : bs.cardinality();
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.view_controller_toggled_marked", new String[]
+ { toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked"),
+ String.valueOf(columnCount),
+ invert ? MessageManager
+ .getString("label.not_containing")
+ : MessageManager.getString("label.containing"),
+ "Highlight", Integer.valueOf(nseq).toString() }));
+ return true;
+ }
+ }
+ else
+ {
+ avcg.setStatus(MessageManager
+ .formatMessage("No highlighted regions marked"));
+ if (!extendCurrent)
+ {
+ cs.clear();
+ alignPanel.paintAlignment(false, false);
+ }
+ }
+ return false;
+ }
+
+}
--- /dev/null
+package jalview.bin;
+
+import jalview.gui.Preferences;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Vector;
+
+/**
+ * Collection of all known applet tags from JalviewLite
+ *
+ * @author hansonr
+ *
+ */
+@SuppressWarnings("serial")
+public class AppletParams extends HashMap<String, String>
+{
+
+ private final static String[] params = { "alignpdbfiles",
+ Preferences.ANNOTATIONCOLOUR_MAX, Preferences.ANNOTATIONCOLOUR_MIN,
+ "annotations",
+ "APPLICATION_URL", "automaticScrolling", "centrecolumnlabels",
+ "debug", "defaultColour", "defaultColourNuc", "defaultColourProt",
+ "embedded", "enableSplitFrame", "externalstructureviewer", "features",
+ "file", "file2", "format", "heightScale", "hidefeaturegroups",
+ "jalviewhelpurl", "jnetfile", "jpredfile", "label", "linkLabel_",
+ "linkLabel_1", "linkURL_", "nojmol", "normaliseLogo",
+ "normaliseSequenceLogo", "oninit", "PDBFILE", "PDBSEQ",
+ "relaxedidmatch", "resolvetocodebase", "RGB", "scaleProteinAsCdna",
+ "scoreFile", "separator", "sequence", "showAnnotation", "showbutton",
+ "showConsensus", "showConsensusHistogram", "showConservation",
+ "showfeaturegroups", "showFeatureSettings", "showFullId",
+ "showGroupConsensus", "showGroupConservation", "showOccupancy",
+ "showQuality", "showSequenceLogo", "showTreeBootstraps",
+ "showTreeDistances", "showUnconserved", "showUnlinkedTreeNodes",
+ "sortBy", "sortByTree", "tree", "treeFile", "upperCase",
+ "userDefinedColour", "widthScale", "windowHeight", "windowWidth",
+ "wrap", };
+
+ public AppletParams(Map<String, String> info)
+ {
+ for (int i = params.length; --i >= 0;)
+ {
+ put(params[i], info.get(params[i]));
+ }
+ }
+
+ public String getParam(String param, String def)
+ {
+ String val = get(param);
+ return (val != null ? val : def);
+ }
+
+ // <applet
+ // code="jalview.bin.JalviewLite" width="140" height="35"
+ // archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
+ // <param name="permissions" value="sandbox"/>
+ // <param name="file" value="uniref50.fa"/>
+ // <param name="treeFile" value="ferredoxin.nw"/>
+ // <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555;
+ // D,E=5555FF"/>
+ // <param name="sortByTree" value="True"/>
+ // <param name="showSequenceLogo" value="true"/>
+ // <param name="showGroupConsensus" value="true"/>
+ // <param name="showFullId" value="false"/>
+ // <param name="linkLabel_1" value="Uniprot"/>
+ // <param name="linkUrl_1"
+ // value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ // <param name="linkLabel_2" value="EMBL-EBI Search"/>
+ // <param name="linkUrl_2"
+ // value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+ // <param name="APPLICATION_URL"
+ // value="http://www.jalview.org/services/launchApp"/>
+ // </applet>
+ //
+ public AppletParams(String outerHTML)
+ {
+ String[] tokens = outerHTML.split("<param");
+ outerHTML = tokens[0];
+ String code = getAttr(outerHTML, "code");
+ if (!code.equals("jalview.bin.JalviewLite"))
+ {
+ return;
+ }
+ for (int i = tokens.length; --i > 0;)
+ {
+ String param = tokens[i];
+ String key = getAttr(param, "name");
+ if (key != null)
+ {
+ String value = getAttr(param, "value");
+ System.out.println("AppletParams " + key + " = \"" + value + "\"");
+ put(key, value);
+ }
+ }
+ put("_width", getAttr(outerHTML, "width"));
+ put("_height", getAttr(outerHTML, "height"));
+ put("_id", getAttr(outerHTML, "id"));
+ put("_name", getAttr(outerHTML, "name"));
+ put("_archive", getAttr(outerHTML, "archive"));
+ put("_code", code);
+ }
+
+ public AppletParams()
+ {
+ // TODO Auto-generated constructor stub
+ }
+
+ public static AppletParams getAppletParams(String[] args,
+ Vector<String> vargs)
+ {
+ AppletParams appletParams = new AppletParams();
+ String resourcePath = null;
+ for (int i = args.length; --i > 0;) // > 0 is correct, not >=0
+ {
+ if (args[i].startsWith("name=\"Info.resourcePath\""))
+ {
+ resourcePath = getAttr(args[i], "value");
+ if (resourcePath.length() > 0 && !resourcePath.endsWith("/"))
+ {
+ resourcePath += "/";
+ }
+ break;
+ }
+ }
+ for (int i = 1; i < args.length; i++)
+ {
+ String arg = args[i].trim();
+ if (arg.startsWith("name="))
+ {
+ String prefName = getAttr(arg, "name");
+ String appletName = prefName.toLowerCase();
+ String argName = prefName;
+ String value = getAttr(arg, "value");
+
+ // note that Application arguments ARE case-sensitive, but
+ // Applet.getParameter() is not.
+
+ switch (appletName)
+ {
+
+ case "file":
+ argName = "open";
+ appletName = null;
+ value = resourcePath + value;
+ break;
+ case "file2":
+ argName = "open2";
+ prefName = null;
+ value = resourcePath + value;
+ break;
+ case "features":
+ case "jnetfile":
+ case "jpredfile":
+ case "pdbfile":
+ case "scorefile":
+ case "sequence":
+ // setting argName to null indicates that we want
+ // JalviewAppLoader to take care of this.
+ prefName = argName = null;
+ value = resourcePath + value;
+ break;
+ case "tree":
+ case "treefile":
+ // setting appletName to null indicates that we want
+ // Jalview.doMain to taken care of this as Jalview args
+ argName = "tree";
+ appletName = null;
+ value = resourcePath + value;
+ break;
+
+ // non-loading preferences
+
+ case "defaultcolour":
+ prefName = Preferences.DEFAULT_COLOUR;
+ break;
+ case "defaultcolournuc":
+ prefName = Preferences.DEFAULT_COLOUR_NUC;
+ break;
+ case "defaultcolourprot":
+ prefName = Preferences.DEFAULT_COLOUR_PROT;
+ break;
+ case "annotationcolour_max":
+ prefName = Preferences.ANNOTATIONCOLOUR_MAX;
+ break;
+ case "annotationcolour_min":
+ prefName = Preferences.ANNOTATIONCOLOUR_MIN;
+ break;
+ case "enablesplitframe":
+ prefName = Preferences.ENABLE_SPLIT_FRAME;
+ break;
+ case "centrecolumnlabels":
+ prefName = Preferences.CENTRE_COLUMN_LABELS;
+ break;
+ case "sortby":
+ prefName = Preferences.SORT_ALIGNMENT; // id, etc.
+ break;
+ case "normalisesequencelogo":
+ prefName = Preferences.NORMALISE_CONSENSUS_LOGO;
+ break;
+ case "relaxedidmatch":
+ prefName = Preferences.RELAXEDSEQIDMATCHING;
+ break;
+ case "scaleproteinascdna":
+ prefName = Preferences.SCALE_PROTEIN_TO_CDNA;
+ break;
+ case "userdefinedcolour":
+ argName = "colour";
+ prefName = Preferences.USER_DEFINED_COLOURS;
+ break;
+ case "wrap":
+ prefName = Preferences.WRAP_ALIGNMENT;
+ break;
+
+ // implemented; not tested:
+
+ case "oninit":
+ prefName = null;
+ break;
+ case "annotations":
+ value = resourcePath + value;
+ argName = null;
+ break;
+ case "hidefeaturegroups":
+ // TODO
+ break;
+ case "pdbseq":
+ argName = prefName = null;
+ break;
+ case "sortbytree":
+ prefName = Preferences.SORT_BY_TREE;
+ value = checkTF(value);
+ appletName = null; // taken care of by Jalview
+ break;
+ case "format":
+ break;
+ case "alignpdbfiles":
+ argName = prefName = null;
+ break;
+ case "separator":
+ break;
+
+ // TODO: probably not relevant?
+
+ case "rgb":
+ prefName = null; // TODO no background for application?
+ break;
+ case "externalstructureviewer":
+ break;
+ case "application_url":
+ break;
+ case "automaticscrolling":
+ break;
+ case "heightscale":
+ break;
+ case "jalviewhelpurl":
+ break;
+ case "label":
+ break;
+ case "linklabel_":
+ prefName = "linkLabel_";
+ break;
+ case "linklabel_1":
+ prefName = "linkLabel_1";
+ break;
+ case "linkurl_":
+ prefName = "linkURL_";
+ break;
+
+ // unknown:
+
+ case "nojmol":
+ case "normaliselogo":
+ case "resolvetocodebase":
+ case "uppercase":
+ case "widthscale":
+ case "windowheight":
+ case "windowwidth":
+ argName = prefName = null;
+ break;
+
+ // TRUE/FALSE
+
+ case "debug":
+ value = checkTF(value);
+ break;
+ case "embedded":
+ value = checkTF(value);
+ break;
+ case "showbutton":
+ value = checkTF(value);
+ break;
+ case "showannotation":
+ prefName = Preferences.SHOW_ANNOTATIONS;
+ value = checkTF(value);
+ break;
+ case "showconsensus":
+ prefName = Preferences.SHOW_CONSENSUS_LOGO;
+ value = checkTF(value);
+ break;
+ case "showconsensushistogram":
+ prefName = Preferences.SHOW_CONSENSUS_HISTOGRAM;
+ value = checkTF(value);
+ break;
+ case "showconservation":
+ prefName = Preferences.SHOW_CONSERVATION;
+ value = checkTF(value);
+ break;
+ case "showgroupconsensus":
+ prefName = Preferences.SHOW_GROUP_CONSENSUS;
+ value = checkTF(value);
+ break;
+ case "showgroupconservation":
+ prefName = Preferences.SHOW_GROUP_CONSERVATION;
+ value = checkTF(value);
+ break;
+ case "showoccupancy":
+ prefName = Preferences.SHOW_OCCUPANCY;
+ value = checkTF(value);
+ break;
+ case "showquality":
+ prefName = Preferences.SHOW_QUALITY;
+ value = checkTF(value);
+ break;
+ case "showsequencelogo":
+ prefName = Preferences.SHOW_CONSENSUS_LOGO;
+ value = checkTF(value);
+ break;
+ case "showfeaturegroups":
+ value = checkTF(value);
+ break;
+ case "showfeaturesettings":
+ value = checkTF(value);
+ break;
+ case "showfullid":
+ value = checkTF(value);
+ break;
+ case "showtreebootstraps":
+ value = checkTF(value);
+ break;
+ case "showtreedistances":
+ value = checkTF(value);
+ break;
+ case "showunconserved":
+ prefName = Preferences.SHOW_UNCONSERVED;
+ value = checkTF(value);
+ break;
+ case "showunlinkedtreenodes":
+ value = checkTF(value);
+ break;
+ default:
+ if (appletName.startsWith("pdbfile")
+ || appletName.startsWith("sequence") && Character.isDigit(
+ appletName.charAt(appletName.length() - 1)))
+ {
+ // could be pdbFile2, for example
+ prefName = argName = null;
+ value = resourcePath + value;
+ break;
+ }
+ // or one of the app preference names
+ break;
+ }
+ // put name and value into application args
+ if (value != null && argName != null)
+ {
+ vargs.add(argName);
+ if (value != "true")
+ {
+ vargs.add(value);
+ }
+ }
+ if (value == null)
+ {
+ value = "false";
+ }
+ System.out.println("AppletParams propName=" + prefName + " argName="
+ + argName + " appletName="
+ + appletName + " value=" + value);
+ if (appletName != null)
+ {
+ appletParams.put(appletName, value);
+ }
+ if (prefName != null)
+ {
+ Cache.setPropertyNoSave(prefName, value);
+ }
+ }
+ }
+ return appletParams;
+ }
+
+ /**
+ * Check for a single-argument option.
+ *
+ * @param value
+ * @return "true" or null
+ */
+ private static String checkTF(String value)
+ {
+ return (value.toLowerCase() == "true" ? "true" : null);
+ }
+
+ /**
+ * Crude applet innerHTML parser
+ *
+ * @param tag
+ * @param attr
+ * @return
+ */
+ private static String getAttr(String tag, String attr)
+ {
+ int pt = tag.indexOf(attr + "=\"");
+ if (pt < 0)
+ {
+ System.out
+ .println("AppletParams did not read " + attr + " in " + tag);
+ return null;
+ }
+ // <param name="sortByTree" value="True"/>
+ int pt1 = pt + attr.length() + 2;
+ int pt2 = tag.indexOf("\"", pt1);
+ return (pt < 0 ? null : tag.substring(pt1, pt2));
+ }
+
+ public static void main(String[] args)
+ {
+ new AppletParams("<applet\r\n"
+ + " code=\"jalview.bin.JalviewLite\" width=\"140\" height=\"35\"\r\n"
+ + " archive=\"jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar\"> \r\n"
+ + " <param name=\"permissions\" value=\"sandbox\"/>\r\n"
+ + " <param name=\"file\" value=\"uniref50.fa\"/>\r\n"
+ + " <param name=\"treeFile\" value=\"ferredoxin.nw\"/>\r\n"
+ + " <param name=\"userDefinedColour\" value=\"C=yellow; R,K,H=FF5555; D,E=5555FF\"/>\r\n"
+ + " <param name=\"sortByTree\" value=\"True\"/>\r\n"
+ + " <param name=\"showSequenceLogo\" value=\"true\"/>\r\n"
+ + " <param name=\"showGroupConsensus\" value=\"true\"/>\r\n"
+ + " <param name=\"showFullId\" value=\"false\"/>\r\n"
+ + " <param name=\"linkLabel_1\" value=\"Uniprot\"/>\r\n"
+ + " <param name=\"linkUrl_1\" value=\"http://www.uniprot.org/uniprot/$SEQUENCE_ID$\"/>\r\n"
+ + " <param name=\"linkLabel_2\" value=\"EMBL-EBI Search\"/>\r\n"
+ + " <param name=\"linkUrl_2\" value=\"http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$\"/>\r\n"
+ + " <param name=\"APPLICATION_URL\" value=\"http://www.jalview.org/services/launchApp\"/>\r\n"
+ + " </applet>");
+ }
+
+}
\ No newline at end of file
*/
public class ArgsParser
{
- Vector<String> vargs = null;
+
+ // BH 2019 - new
+
+ public static final String NOCALCULATION = "nocalculation";
+
+ public static final String NOMENUBAR = "nomenubar";
+
+ public static final String NOSTATUS = "nostatus";
+
+ public static final String SHOWOVERVIEW = "showoverview";
+
+ //
+ public static final String ANNOTATIONS = "annotations";
+
+ public static final String COLOUR = "colour";
+
+ public static final String FEATURES = "features";
+
+ public static final String GROOVY = "groovy";
+
+ public static final String GROUPS = "groups";
+
+ public static final String HEADLESS = "headless";
+
+ public static final String JABAWS = "jabaws";
+
+ public static final String NOANNOTATION = "no-annotation";
+
+ public static final String NOANNOTATION2 = "noannotation"; // BH 2019.05.07
+
+ public static final String NODISPLAY = "nodisplay";
+
+ public static final String NOGUI = "nogui";
+
+ public static final String NONEWS = "nonews";
+
+ public static final String NOQUESTIONNAIRE = "noquestionnaire";
+
+ public static final String NOSORTBYTREE = "nosortbytree";
+
+ public static final String NOUSAGESTATS = "nousagestats";
+
+ public static final String OPEN = "open";
+
+ public static final String OPEN2 = "open2"; // BH added -- for applet
+ // compatibility; not fully
+ // implemented
+
+ public static final String PROPS = "props";
+
+ public static final String QUESTIONNAIRE = "questionnaire";
+
+ public static final String SETPROP = "setprop";
+
+ public static final String SORTBYTREE = "sortbytree";
+
+ public static final String TREE = "tree";
+
+ public static final String VDOC = "vdoc";
+
+ public static final String VSESS = "vsess";
+
+ private Vector<String> vargs = null;
+
+ private boolean isApplet;
+
+ private AppletParams appletParams;
+
+ public boolean isApplet()
+ {
+ return isApplet;
+ }
public ArgsParser(String[] args)
{
- vargs = new Vector<String>();
- for (int i = 0; i < args.length; i++)
+ vargs = new Vector<>();
+ isApplet = (args.length > 0 && args[0].startsWith("<applet"));
+ if (isApplet)
+ {
+ appletParams = AppletParams.getAppletParams(args, vargs);
+ }
+ else
{
- String arg = args[i].trim();
- if (arg.charAt(0) == '-')
+ for (int i = 0; i < args.length; i++)
{
- arg = arg.substring(1);
+ String arg = args[i].trim();
+ if (arg.charAt(0) == '-')
+ {
+ arg = arg.substring(1);
+ }
+ vargs.addElement(arg);
}
- vargs.addElement(arg);
}
}
return vargs.size();
}
+ public String getAppletValue(String key, String def)
+ {
+ String value;
+ return (appletParams == null ? null
+ : (value = appletParams.get(key.toLowerCase())) != null ? value
+ : def);
+ }
+
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.gui;
+
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.util.MessageManager;
+
+/**
+ * GUI related routines for associating PDB files with sequences. A single
+ * static method.
+ *
+ * @author JimP
+ *
+ */
+public class AssociatePdbFileWithSeq
+{
+
+ private AssociatePdbFileWithSeq()
+ {
+ // inaccessible
+ }
+
+ /**
+ * Associate the given PDB file name or URL with a sequence. Do not map
+ * mouse-over events.
+ *
+ * @param fileName
+ * or URL
+ * @param type
+ * will be DataType.FILE or DataType.URL
+ * @param sequence
+ * to associate
+ * @param prompt
+ * true if the user should be asked what to do if the specified file
+ * does not seem to contain PDB information (StructureChooser only)
+ * @return null if file is not found
+ */
+ public static PDBEntry associatePdbWithSeq(String fileName,
+ DataSourceType type, SequenceI sequence, boolean prompt)
+ {
+ PDBEntry entry = new PDBEntry();
+ StructureFile pdbfile = null;
+ pdbfile = Desktop.getStructureSelectionManager()
+ .setMapping(false, new SequenceI[]
+ { sequence }, null, fileName, type);
+ if (pdbfile == null)
+ {
+ // stacktrace already thrown so just return
+ return null;
+ }
+ String id = pdbfile.getId();
+ if (id == null && (id = (prompt
+ ? JvOptionPane.showInternalInputDialog(Desktop.getDesktopPane(),
+ MessageManager
+ .getString("label.couldnt_find_pdb_id_in_file"),
+ MessageManager.getString("label.no_pdb_id_in_file"),
+ JvOptionPane.QUESTION_MESSAGE)
+ : null)) == null)
+ {
+ return null;
+ }
+ entry.setId(id);
+ entry.setType(PDBEntry.Type.FILE);
+ entry.setFile(fileName);
+ sequence.getDatasetSequence().addPDBId(entry);
+ Desktop.getInstance().getStructureSelectionManager()
+ .registerPDBEntry(entry);
+ return entry;
+ }
+}
*/
package jalview.bin;
+import jalview.api.AlignCalcWorkerI;
+import jalview.api.AlignFrameI;
+import jalview.api.AlignViewportI;
+import jalview.api.JalviewApp;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.CalculationChooser;
import jalview.gui.Desktop;
+import jalview.gui.Preferences;
import jalview.gui.PromptUserConfig;
+import jalview.gui.StructureViewer;
import jalview.io.AppletFormatAdapter;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FileLoader;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
import jalview.io.gff.SequenceOntologyFactory;
+import jalview.javascript.JSFunctionExec;
+import jalview.javascript.MouseOverStructureListener;
+import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+import jalview.structure.SelectionSource;
+import jalview.structure.VamsasSource;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.jws2.Jws2Discoverer;
+import java.applet.AppletContext;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.security.Permissions;
import java.security.Policy;
import java.util.HashMap;
+import java.util.Hashtable;
import java.util.Map;
import java.util.Vector;
-import java.util.logging.ConsoleHandler;
-import java.util.logging.Level;
-import java.util.logging.Logger;
import javax.swing.LookAndFeel;
+import javax.swing.SwingUtilities;
import javax.swing.UIManager;
-import com.threerings.getdown.util.LaunchUtil;
-
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
+import netscape.javascript.JSObject;
/**
* Main class for Jalview Application <br>
* @author $author$
* @version $Revision$
*/
-public class Jalview
+public class Jalview implements ApplicationSingletonI, JalviewJSApi
{
+
+ public static Jalview getInstance()
+ {
+ return (Jalview) ApplicationSingletonProvider
+ .getInstance(Jalview.class);
+ }
+
+ private Jalview()
+ {
+ }
+
static
{
Platform.getURLCommandArguments();
}
- // singleton instance of this class
+ private boolean headless;
- private static Jalview instance;
+ public static boolean isHeadlessMode()
+ {
+ return getInstance().headless;
+ }
private Desktop desktop;
- public static AlignFrame currentAlignFrame;
+ private AlignFrame currentAlignFrame;
+
+ public boolean isJavaAppletTag;
+
+ public String appletResourcePath;
+
+ JalviewAppLoader appLoader;
+
+ protected JSFunctionExec jsFunctionExec;
+
+ private boolean noCalculation, noMenuBar, noStatus;
+
+ private boolean noAnnotation;
+
+ public static final String TERMINATOR_LINE = "Jalview argument parsing complete.";
+
+ public boolean getStartCalculations()
+ {
+ return !noCalculation;
+ }
+
+ public boolean getAllowMenuBar()
+ {
+ return !noMenuBar;
+ }
+
+ public boolean getShowStatus()
+ {
+ return !noStatus;
+ }
+
+ public boolean getShowAnnotation()
+ {
+ return !noAnnotation;
+ }
+
+ public static AlignFrame getCurrentAlignFrame()
+ {
+ return getInstance().currentAlignFrame;
+ }
+
+ public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
+ {
+ getInstance().currentAlignFrame = currentAlignFrame;
+ }
static
{
*/
{
// grab all the rights we can for the JVM
- Policy.setPolicy(new Policy()
- {
- @Override
- public PermissionCollection getPermissions(CodeSource codesource)
- {
- Permissions perms = new Permissions();
- perms.add(new AllPermission());
- return (perms);
- }
-
- @Override
- public void refresh()
- {
- }
- });
+ Policy.setPolicy(new Policy()
+ {
+ @Override
+ public PermissionCollection getPermissions(CodeSource codesource)
+ {
+ Permissions perms = new Permissions();
+ perms.add(new AllPermission());
+ return (perms);
+ }
+
+ @Override
+ public void refresh()
+ {
+ }
+ });
}
}
class FeatureFetcher
{
/*
- * TODO: generalise to track all jalview events to orchestrate batch processing
- * events.
+ * TODO: generalise to track all jalview events to orchestrate batch
+ * processing events.
*/
private int queued = 0;
}
- public static Jalview getInstance()
- {
- return instance;
- }
-
/**
* main class for Jalview application
*
* @param args
- * open <em>filename</em>
+ * open <em>filename</em>
*/
public static void main(String[] args)
{
-// setLogging(); // BH - for event debugging in JavaScript
- instance = new Jalview();
- instance.doMain(args);
-}
-
- private static void logClass(String name)
- {
- // BH - for event debugging in JavaScript
- ConsoleHandler consoleHandler = new ConsoleHandler();
- consoleHandler.setLevel(Level.ALL);
- Logger logger = Logger.getLogger(name);
- logger.setLevel(Level.ALL);
- logger.addHandler(consoleHandler);
- }
-
- @SuppressWarnings("unused")
- private static void setLogging()
- {
-
- /**
- * @j2sIgnore
- *
- */
- {
- System.out.println("not in js");
- }
-
- // BH - for event debugging in JavaScript (Java mode only)
- if (!Platform.isJS())
- /**
- * Java only
- *
- * @j2sIgnore
- */
- {
- Logger.getLogger("").setLevel(Level.ALL);
- logClass("java.awt.EventDispatchThread");
- logClass("java.awt.EventQueue");
- logClass("java.awt.Component");
- logClass("java.awt.focus.Component");
- logClass("java.awt.focus.DefaultKeyboardFocusManager");
- }
-
+ // Platform.startJavaLogging();
+ getInstance().doMain(args);
}
-
-
+ @SuppressWarnings("unused")
/**
* @param args
*/
void doMain(String[] args)
{
- if (!Platform.isJS())
+ boolean isJS = Platform.isJS();
+ if (isJS)
+ {
+ Platform.setAppClass(this);
+ }
+ else
{
System.setSecurityManager(null);
}
System.out
- .println("Java version: "
- + System.getProperty("java.version"));
- System.out.println("Java Home: " + System.getProperty("java.home"));
+ .println("Java version: " + System.getProperty("java.version"));
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
- String val = System.getProperty("sys.install4jVersion");
- if (val != null) {
- System.out.println("Install4j version: " + val);
- }
- val = System.getProperty("installer_template_version");
- if (val != null) {
- System.out.println("Install4j template version: " + val);
- }
- val = System.getProperty("launcher_version");
- if (val != null) {
- System.out.println("Launcher version: " + val);
- }
-
- // report Jalview version
- Cache.loadBuildProperties(true);
ArgsParser aparser = new ArgsParser(args);
- boolean headless = false;
- String usrPropsFile = aparser.getValue("props");
- Cache.loadProperties(usrPropsFile); // must do this before
- if (usrPropsFile != null)
+ String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
+ Cache.loadProperties(usrPropsFile);
+
+ if (aparser.contains(ArgsParser.NODISPLAY)
+ || aparser.contains(ArgsParser.NOGUI)
+ || aparser.contains(ArgsParser.HEADLESS)
+ || "true".equals(System.getProperty("java.awt.headless")))
{
- System.out.println(
- "CMD [-props " + usrPropsFile + "] executed successfully!");
+ headless = true;
+ setSynchronous(true);
}
- if (!Platform.isJS())
+ if (isJS)
+ {
+ isJavaAppletTag = aparser.isApplet();
+ if (isJavaAppletTag)
+ {
+ Preferences.setAppletDefaults();
+ Cache.loadProperties(usrPropsFile); // again, because we
+ // might be changing defaults here?
+ }
+ System.out.println(
+ "<Applet> found: " + aparser.getValue("Info.j2sAppletID"));
+ appletResourcePath = aparser.getValue("Info.resourcePath");
+ }
+ else
/**
* Java only
*
* @j2sIgnore
*/
{
+ if (usrPropsFile != null)
+ {
+ System.out.println(
+ "CMD [-props " + usrPropsFile + "] executed successfully!");
+ }
+
if (aparser.contains("help") || aparser.contains("h"))
{
showUsage();
System.exit(0);
}
- if (aparser.contains("nodisplay") || aparser.contains("nogui")
- || aparser.contains("headless"))
- {
- System.setProperty("java.awt.headless", "true");
- headless = true;
- }
+
// anything else!
- final String jabawsUrl = aparser.getValue("jabaws");
+ final String jabawsUrl = aparser.getValue(ArgsParser.JABAWS);
if (jabawsUrl != null)
{
try
{
- Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+ Jws2Discoverer.getInstance().setPreferredUrl(jabawsUrl);
System.out.println(
"CMD [-jabaws " + jabawsUrl + "] executed successfully!");
} catch (MalformedURLException e)
}
}
- String defs = aparser.getValue("setprop");
+ // check for property setting
+ String defs = aparser.getValue(ArgsParser.SETPROP);
while (defs != null)
{
int p = defs.indexOf('=');
else
{
System.out.println("Executing setprop argument: " + defs);
- if (Platform.isJS())
+ if (isJS)
{
- Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
+ Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
}
}
- defs = aparser.getValue("setprop");
- }
- if (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"))
- {
- headless = true;
+ defs = aparser.getValue(ArgsParser.SETPROP);
}
System.setProperty("http.agent",
"Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
try
{
- UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+ if (!isJS && Platform.isWin())
+ {
+ UIManager.setLookAndFeel(
+ headless ? "javax.swing.plaf.metal.MetalLookAndFeel"
+ : UIManager.getSystemLookAndFeelClassName());
+ // UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+ }
} catch (Exception ex)
{
System.err.println("Unexpected Look and Feel Exception");
}
/*
- * configure 'full' SO model if preferences say to, else use the default (full SO)
- * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
+ * configure 'full' SO model if preferences say to,
+ * else use the default (SO Lite)
*/
- boolean soDefault = !Platform.isJS();
- if (Cache.getDefault("USE_FULL_SO", soDefault))
+ if (Cache.getDefault(Preferences.USE_FULL_SO, false))
{
- SequenceOntologyFactory.setInstance(new SequenceOntology());
+ SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
}
- if (!headless)
+ if (headless)
{
- desktop = new Desktop();
- desktop.setInBatchMode(true); // indicate we are starting up
+ // If this is not tested, then
- try
+ if (aparser.contains(ArgsParser.NOUSAGESTATS))
{
- JalviewTaskbar.setTaskbar(this);
- } catch (Throwable t)
+ System.err.println("CMD [-nousagestats] executed successfully!");
+ }
+ if (aparser.contains(ArgsParser.NOQUESTIONNAIRE))
{
- System.out.println("Error setting Taskbar: " + t.getMessage());
+ System.err.println("CMD [-noquestionnaire] executed successfully!");
}
+ }
+ else
+ {
+ desktop = Desktop.getInstance();
+ desktop.setInBatchMode(true); // indicate we are starting up
desktop.setVisible(true);
- if (!Platform.isJS())
+ if (!isJS)
/**
* Java only
*
*/
{
desktop.startServiceDiscovery();
- if (!aparser.contains("nousagestats"))
+ if (!aparser.contains(ArgsParser.NOUSAGESTATS))
{
startUsageStats(desktop);
}
System.err.println("CMD [-nousagestats] executed successfully!");
}
- if (!aparser.contains("noquestionnaire"))
+ if (!aparser.contains(ArgsParser.NOQUESTIONNAIRE))
{
- String url = aparser.getValue("questionnaire");
+ String url = aparser.getValue(ArgsParser.QUESTIONNAIRE);
if (url != null)
{
// Start the desktop questionnaire prompter with the specified
}
else
{
- if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+ if (Cache.getProperty(Preferences.NOQUESTIONNAIRES) == null)
{
// Start the desktop questionnaire prompter with the specified
// questionnaire
.println("CMD [-noquestionnaire] executed successfully!");
}
- if (!aparser.contains("nonews"))
+ if (!aparser.contains(ArgsParser.NONEWS))
{
desktop.checkForNews();
}
}
}
- // Move any new getdown-launcher-new.jar into place over old
- // getdown-launcher.jar
- String appdirString = System.getProperty("getdownappdir");
- if (appdirString != null && appdirString.length() > 0)
+ parseArguments(aparser, true);
+ System.err.println(TERMINATOR_LINE);
+ }
+
+ /**
+ * Allow an outside entity to initiate the second half of argument parsing
+ * (only).
+ *
+ * @param args
+ * @return null is good
+ */
+ @Override
+ public Object parseArguments(String[] args)
+ {
+
+ try
{
- final File appdir = new File(appdirString);
- new Thread()
- {
- @Override
- public void run()
- {
- LaunchUtil.upgradeGetdown(
- new File(appdir, "getdown-launcher-old.jar"),
- new File(appdir, "getdown-launcher.jar"),
- new File(appdir, "getdown-launcher-new.jar"));
- }
- }.start();
+ ArgsParser aparser = new ArgsParser(args);
+ return parseArguments(aparser, false);
+ } catch (Throwable t)
+ {
+ return t;
}
+ }
- String file = null, data = null;
- FileFormatI format = null;
- DataSourceType protocol = null;
- FileLoader fileLoader = new FileLoader(!headless);
+ /**
+ *
+ * @param aparser
+ * @param isStartup
+ * @return
+ */
+ private Object parseArguments(ArgsParser aparser, boolean isStartup)
+ {
+ boolean isJS = Platform.isJS();
- String groovyscript = null; // script to execute after all loading is
+ Desktop desktop = (headless ? null : Desktop.getInstance());
+ // script to execute after all loading is
// completed one way or another
// extract groovy argument and execute if necessary
- groovyscript = aparser.getValue("groovy", true);
- file = aparser.getValue("open", true);
+ String groovyscript = (isJS ? null
+ : aparser.getValue(ArgsParser.GROOVY, true));
+ String file = aparser.getValue(ArgsParser.OPEN, true);
+ // BH this here to allow split frame; not working as of 5/17/2019
+ String file2 = aparser.getValue(ArgsParser.OPEN2, true);
+ String fileFormat = (isJavaAppletTag
+ ? aparser.getAppletValue("format", null)
+ : null);
+ FileFormatI format = null;
+ DataSourceType protocol = null;
if (file == null && desktop == null)
{
System.out.println("No files to open!");
System.exit(1);
}
- long progress = -1;
+ boolean haveImport = false;// checkStartVamas(aparser);
// Finally, deal with the remaining input data.
+ long progress = -1;
+ if (file == null && isJavaAppletTag)
+ {
+ // Maybe the sequences are added as parameters
+ StringBuffer data = new StringBuffer("PASTE");
+ int i = 1;
+ while ((file = aparser.getAppletValue("sequence" + i, null)) != null)
+ {
+ data.append(file.toString() + "\n");
+ i++;
+ }
+ if (data.length() > 5)
+ {
+ file = data.toString();
+ }
+ }
+
+ String data;
+
if (file != null)
{
+
if (!headless)
{
desktop.setProgressBar(
.getString("status.processing_commandline_args"),
progress = System.currentTimeMillis());
}
- System.out.println("CMD [-open " + file + "] executed successfully!");
- if (!Platform.isJS())
- /**
- * ignore in JavaScript -- can't just file existence - could load it?
- *
- * @j2sIgnore
- */
+ if (!isJS)
+ /**
+ * ignore in JavaScript -- can't just check file existence - could load
+ * it?
+ *
+ * @j2sIgnore
+ */
{
if (!file.startsWith("http://") && !file.startsWith("https://"))
// BH 2019 added https check for Java
}
}
- protocol = AppletFormatAdapter.checkProtocol(file);
+ protocol = AppletFormatAdapter.checkProtocol(file);
try
{
- format = new IdentifyFile().identify(file, protocol);
+ format = (isJavaAppletTag && fileFormat != null
+ ? FileFormats.getInstance().forName(fileFormat)
+ : null);
+ if (format == null)
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ }
} catch (FileFormatException e1)
{
// TODO ?
}
- AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
- format);
+ if (aparser.contains(ArgsParser.NOMENUBAR))
+ {
+ noMenuBar = true;
+ System.out.println("CMD [nomenu] executed successfully!");
+ }
+
+ if (aparser.contains(ArgsParser.NOSTATUS))
+ {
+ noStatus = true;
+ System.out.println("CMD [nostatus] executed successfully!");
+ }
+
+ if (aparser.contains(ArgsParser.NOANNOTATION)
+ || aparser.contains(ArgsParser.NOANNOTATION2))
+ {
+ noAnnotation = true;
+ System.out.println("CMD no-annotation executed successfully!");
+ }
+ if (aparser.contains(ArgsParser.NOCALCULATION))
+ {
+ noCalculation = true;
+ System.out.println("CMD [nocalculation] executed successfully!");
+ }
+
+ AlignFrame af = new FileLoader(!headless).LoadFileWaitTillLoaded(file,
+ protocol, format);
if (af == null)
{
System.out.println("error");
}
else
{
+ System.out
+ .println("CMD [-open " + file + "] executed successfully!");
+ if (file2 != null)
+ {
+ protocol = AppletFormatAdapter.checkProtocol(file2);
+ try
+ {
+ format = new IdentifyFile().identify(file2, protocol);
+ } catch (FileFormatException e1)
+ {
+ // TODO ?
+ }
+ AlignFrame af2 = new FileLoader(!headless)
+ .LoadFileWaitTillLoaded(file2, protocol, format);
+ if (af2 == null)
+ {
+ System.out.println("error");
+ }
+ else
+ {
+ AlignViewport.openLinkedAlignmentAs(af,
+ af.getViewport().getAlignment(),
+ af2.getViewport().getAlignment(), "",
+ AlignViewport.SPLIT_FRAME);
+ System.out.println(
+ "CMD [-open2 " + file2 + "] executed successfully!");
+ }
+ }
+
setCurrentAlignFrame(af);
- data = aparser.getValue("colour", true);
+
+ // TODO: file2 How to implement file2 for the applet spit screen?
+
+ data = aparser.getValue(ArgsParser.COLOUR, true);
if (data != null)
{
data.replaceAll("%20", " ");
}
// Must maintain ability to use the groups flag
- data = aparser.getValue("groups", true);
+ data = aparser.getValue(ArgsParser.GROUPS, true);
if (data != null)
{
af.parseFeaturesFile(data,
System.out.println(
"CMD groups[-" + data + "] executed successfully!");
}
- data = aparser.getValue("features", true);
+ data = aparser.getValue(ArgsParser.FEATURES, true);
if (data != null)
{
af.parseFeaturesFile(data,
"CMD [-features " + data + "] executed successfully!");
}
- data = aparser.getValue("annotations", true);
+ data = aparser.getValue(ArgsParser.ANNOTATIONS, true);
if (data != null)
{
af.loadJalviewDataFile(data, null, null, null);
System.out.println(
"CMD [-annotations " + data + "] executed successfully!");
}
+
+ if (aparser.contains(ArgsParser.SHOWOVERVIEW))
+ {
+ af.overviewMenuItem_actionPerformed(null);
+ System.out.println("CMD [showoverview] executed successfully!");
+ }
+
// set or clear the sortbytree flag.
- if (aparser.contains("sortbytree"))
+ if (aparser.contains(ArgsParser.SORTBYTREE))
{
af.getViewport().setSortByTree(true);
if (af.getViewport().getSortByTree())
System.out.println("CMD [-sortbytree] executed successfully!");
}
}
- if (aparser.contains("no-annotation"))
+
+ boolean doUpdateAnnotation = false;
+
+ /**
+ * we do this earlier in JalviewJS because of a complication with
+ * SHOWOVERVIEW
+ *
+ * For now, just fixing this in JalviewJS.
+ *
+ *
+ * @j2sIgnore
+ *
+ */
{
- af.getViewport().setShowAnnotation(false);
- if (!af.getViewport().isShowAnnotation())
+ if (aparser.contains(ArgsParser.NOANNOTATION)
+ || aparser.contains(ArgsParser.NOANNOTATION2))
{
- System.out.println("CMD no-annotation executed successfully!");
+ af.getViewport().setShowAnnotation(false);
+ if (!af.getViewport().isShowAnnotation())
+ {
+ doUpdateAnnotation = true;
+ System.out
+ .println("CMD no-annotation executed successfully!");
+ }
}
}
- if (aparser.contains("nosortbytree"))
+ if (aparser.contains(ArgsParser.NOSORTBYTREE))
{
af.getViewport().setSortByTree(false);
if (!af.getViewport().getSortByTree())
{
+ doUpdateAnnotation = true;
System.out
.println("CMD [-nosortbytree] executed successfully!");
}
}
- data = aparser.getValue("tree", true);
+ if (doUpdateAnnotation)
+ { // BH 2019.07.24
+ af.setMenusForViewport();
+ af.alignPanel.updateLayout();
+ }
+ data = aparser.getValue(ArgsParser.TREE, true);
if (data != null)
{
try
// TODO - load PDB structure(s) to alignment JAL-629
// (associate with identical sequence in alignment, or a specified
// sequence)
- if (groovyscript != null)
+ if (isJavaAppletTag)
{
- // Execute the groovy script after we've done all the rendering stuff
- // and before any images or figures are generated.
- System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, af);
- System.out.println("CMD groovy[" + groovyscript
- + "] executed successfully!");
- groovyscript = null;
+ loadAppletParams(aparser, af);
}
- String imageName = "unnamed.png";
- while (aparser.getSize() > 1)
+ else if (!isJS)
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- String outputFormat = aparser.nextValue();
- file = aparser.nextValue();
-
- if (outputFormat.equalsIgnoreCase("png"))
- {
- af.createPNG(new File(file));
- imageName = (new File(file)).getName();
- System.out.println("Creating PNG image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("svg"))
- {
- File imageFile = new File(file);
- imageName = imageFile.getName();
- af.createSVG(imageFile);
- System.out.println("Creating SVG image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("html"))
- {
- File imageFile = new File(file);
- imageName = imageFile.getName();
- HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- htmlSVG.exportHTML(file);
-
- System.out.println("Creating HTML image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("biojsmsa"))
- {
- if (file == null)
- {
- System.err.println("The output html file must not be null");
- return;
- }
- try
- {
- BioJsHTMLOutput.refreshVersionInfo(
- BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
- } catch (URISyntaxException e)
- {
- e.printStackTrace();
- }
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
- bjs.exportHTML(file);
- System.out
- .println("Creating BioJS MSA Viwer HTML file: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("imgMap"))
- {
- af.createImageMap(new File(file), imageName);
- System.out.println("Creating image map: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("eps"))
- {
- File outputFile = new File(file);
- System.out.println(
- "Creating EPS file: " + outputFile.getAbsolutePath());
- af.createEPS(outputFile);
- continue;
- }
-
- af.saveAlignment(file, format);
- if (af.isSaveAlignmentSuccessful())
- {
- System.out.println("Written alignment in " + format
- + " format to " + file);
- }
- else
+ if (groovyscript != null)
{
- System.out.println("Error writing file " + file + " in "
- + format + " format!!");
+ // Execute the groovy script after we've done all the rendering
+ // stuff
+ // and before any images or figures are generated.
+ System.out.println("Executing script " + groovyscript);
+ executeGroovyScript(groovyscript, af);
+ System.out.println("CMD groovy[" + groovyscript
+ + "] executed successfully!");
+ groovyscript = null;
}
-
}
-
+ createOutputFiles(aparser, af, format);
while (aparser.getSize() > 0)
{
System.out.println("Unknown arg: " + aparser.nextValue());
// And the user
// ////////////////////
- if (!Platform.isJS() && !headless && file == null
- && Cache.getDefault("SHOW_STARTUP_FILE", true))
+ if (!isJS && !headless && file == null && !haveImport
+ && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
/**
* Java only
*
* @j2sIgnore
*/
{
- file = Cache.getDefault("STARTUP_FILE",
- Cache.getDefault("www.jalview.org",
+ file = jalview.bin.Cache.getDefault("STARTUP_FILE",
+ jalview.bin.Cache.getDefault("www.jalview.org",
"http://www.jalview.org")
+ "/examples/exampleFile_2_7.jar");
if (file.equals(
// hardwire upgrade of the startup file
file.replace("_2_3.jar", "_2_7.jar");
// and remove the stale setting
- Cache.removeProperty("STARTUP_FILE");
+ jalview.bin.Cache.removeProperty("STARTUP_FILE");
}
protocol = DataSourceType.FILE;
}
}
- startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
- format);
+ startUpAlframe = new FileLoader(!headless)
+ .LoadFileWaitTillLoaded(file, protocol, format);
// extract groovy arguments before anything else.
}
}
desktop.setInBatchMode(false);
}
+
+ return null;
}
- private static void showUsage()
+ /**
+ * Writes an output file for each format (if any) specified in the
+ * command-line arguments. Supported formats are currently
+ * <ul>
+ * <li>png</li>
+ * <li>svg</li>
+ * <li>html</li>
+ * <li>biojsmsa</li>
+ * <li>imgMap</li>
+ * <li>eps</li>
+ * </ul>
+ * A format parameter should be followed by a parameter specifying the output
+ * file name. {@code imgMap} parameters should follow those for the
+ * corresponding alignment image output.
+ *
+ * @param aparser
+ * @param af
+ * @param format
+ */
+ private void createOutputFiles(ArgsParser aparser, AlignFrame af,
+ FileFormatI format)
{
- System.out.println(
- "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
- + "-nodisplay\tRun Jalview without User Interface.\n"
- + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
- + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
- + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
- + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
- + "-features FILE\tUse the given file to mark features on the alignment.\n"
- + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
- + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
- + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
- + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
- + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
- + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
- + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
- + "-json FILE\tCreate alignment file FILE in JSON format.\n"
- + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
- + "-png FILE\tCreate PNG image FILE from alignment.\n"
- + "-svg FILE\tCreate SVG image FILE from alignment.\n"
- + "-html FILE\tCreate HTML file from alignment.\n"
- + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
- + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
- + "-eps FILE\tCreate EPS file FILE from alignment.\n"
- + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
+ String imageName = "unnamed.png";
+ while (aparser.getSize() > 1)
+ {
+ String outputFormat = aparser.nextValue();
+ String file = aparser.nextValue();
+ // System.out.println("format " + outputFormat);
+
+ if (outputFormat.equalsIgnoreCase("png"))
+ {
+ af.createPNG(new File(file));
+ imageName = (new File(file)).getName();
+ System.out.println("Creating PNG image: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("svg"))
+ {
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ af.createSVG(imageFile);
+ System.out.println("Creating SVG image: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("html"))
+ {
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+ htmlSVG.exportHTML(file);
+
+ System.out.println("Creating HTML image: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("biojsmsa"))
+ {
+ if (file == null)
+ {
+ System.err.println("The output html file must not be null");
+ return;
+ }
+ try
+ {
+ BioJsHTMLOutput.refreshVersionInfo(
+ BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
+ {
+ e.printStackTrace();
+ }
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+ bjs.exportHTML(file);
+ System.out.println("Creating BioJS MSA Viwer HTML file: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("imgMap"))
+ {
+ af.createImageMap(new File(file), imageName);
+ System.out.println("Creating image map: " + file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("eps"))
+ {
+ File outputFile = new File(file);
+ System.out.println(
+ "Creating EPS file: " + outputFile.getAbsolutePath());
+ af.createEPS(outputFile);
+ continue;
+ }
+
+ af.saveAlignment(file, format);
+ if (af.isSaveAlignmentSuccessful())
+ {
+ System.out.println(
+ "Written alignment in " + format + " format to " + file);
+ }
+ else
+ {
+ System.out.println("Error writing file " + file + " in " + format
+ + " format!!");
+ }
+
+ }
+ }
+
+ private static void showUsage()
+ {
+ System.out.println(
+ "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
+ + "-nodisplay\tRun Jalview without User Interface.\n"
+ + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
+ + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
+ + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
+ + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
+ + "-features FILE\tUse the given file to mark features on the alignment.\n"
+ + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
+ + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
+ + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
+ + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
+ + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
+ + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
+ + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
+ + "-json FILE\tCreate alignment file FILE in JSON format.\n"
+ + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
+ + "-png FILE\tCreate PNG image FILE from alignment.\n"
+ + "-svg FILE\tCreate SVG image FILE from alignment.\n"
+ + "-html FILE\tCreate HTML file from alignment.\n"
+ + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
+ + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
+ + "-eps FILE\tCreate EPS file FILE from alignment.\n"
+ + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
+ "-noquestionnaire\tTurn off questionnaire check.\n"
+ "-nonews\tTurn off check for Jalview news.\n"
+ "-nousagestats\tTurn off google analytics tracking for this session.\n"
// passed in correctly)"
+ "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
+ "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
+ // +
+ // "-vdoc vamsas-document\tImport vamsas document into new
+ // session or join existing session with same URN\n"
+ // + "-vses vamsas-session\tJoin session with given URN\n"
+ "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
+ "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
}
/**
* start a User Config prompt asking if we can log usage statistics.
*/
- PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
- "USAGESTATS", "Jalview Usage Statistics",
+ PromptUserConfig prompter = new PromptUserConfig(
+ Desktop.getDesktopPane(), "USAGESTATS",
+ "Jalview Usage Statistics",
"Do you want to help make Jalview better by enabling "
+ "the collection of usage statistics with Google Analytics ?"
+ "\n\n(you can enable or disable usage tracking in the preferences)",
* Locate the given string as a file and pass it to the groovy interpreter.
*
* @param groovyscript
- * the script to execute
+ * the script to execute
* @param jalviewContext
- * the Jalview Desktop object passed in to the groovy
- * binding as the 'Jalview' object.
+ * the Jalview Desktop object passed in to the groovy binding as the
+ * 'Jalview' object.
*/
private void executeGroovyScript(String groovyscript, AlignFrame af)
{
}
try
{
- Map<String, java.lang.Object> vbinding = new HashMap<>();
+ Map<String, Object> vbinding = new HashMap<>();
vbinding.put("Jalview", this);
if (af != null)
{
}
}
- public static boolean isHeadlessMode()
- {
- String isheadless = System.getProperty("java.awt.headless");
- if (isheadless != null && isheadless.equalsIgnoreCase("true"))
- {
- return true;
- }
- return false;
- }
-
public AlignFrame[] getAlignFrames()
{
return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
}
/**
- * Quit method delegates to Desktop.quit - unless running in headless mode when
- * it just ends the JVM
+ * Quit method delegates to Desktop.quit - unless running in headless mode
+ * when it just ends the JVM
*/
public void quit()
{
+ if (jsFunctionExec != null)
+ {
+ jsFunctionExec.tidyUp();
+ jsFunctionExec = null;
+ }
+
if (desktop != null)
{
desktop.quit();
}
}
- public static AlignFrame getCurrentAlignFrame()
+ /**
+ * Handle all JalviewLite applet parameters
+ *
+ * @param aparser
+ * @param af
+ */
+ private void loadAppletParams(ArgsParser aparser, AlignFrame af)
+ {
+ JalviewApp app = new JalviewApp()
+ {
+
+ // TODO BH 2019
+ //
+ // These are methods that are in JalviewLite that various classes call
+ // but are not in JalviewLiteJsApi. Or, even if they are, other classes
+ // call
+ // them to JalviewLite directly. Some may not be necessary, but they have
+ // to
+ // be at least mentioned here, or the classes calling them should
+ // reference
+ // JalviewLite itself.
+
+ private boolean alignPDBStructures; // From JalviewLite; not implemented
+
+ private Hashtable<String, Hashtable<String, String[]>> jsmessages;
+
+ private Hashtable<String, int[]> jshashes;
+
+ @Override
+ public String getParameter(String name)
+ {
+ return aparser.getAppletValue(name, null);
+ }
+
+ @Override
+ public boolean getDefaultParameter(String name, boolean def)
+ {
+ String stn;
+ return ((stn = getParameter(name)) == null ? def
+ : "true".equalsIgnoreCase(stn));
+ }
+
+ /**
+ * Get the applet-like document base even though this is an application.
+ */
+ @Override
+ public URL getDocumentBase()
+ {
+ return Platform.getDocumentBase();
+ }
+
+ /**
+ * Get the applet-like code base even though this is an application.
+ */
+ @Override
+ public URL getCodeBase()
+ {
+ return Platform.getCodeBase();
+ }
+
+ @Override
+ public AlignViewportI getViewport()
+ {
+ return af.getViewport();
+ }
+
+ /**
+ * features
+ *
+ */
+ @Override
+ public boolean parseFeaturesFile(String filename,
+ DataSourceType protocol)
+ {
+ return af.parseFeaturesFile(filename, protocol);
+ }
+
+ /**
+ * scorefile
+ *
+ */
+ @Override
+ public boolean loadScoreFile(String sScoreFile) throws IOException
+ {
+ af.loadJalviewDataFile(sScoreFile, null, null, null);
+ return true;
+ }
+
+ /**
+ * annotations, jpredfile, jnetfile
+ *
+ */
+ @Override
+ public void updateForAnnotations()
+ {
+ af.updateForAnnotations();
+ }
+
+ @Override
+ public void loadTree(NewickFile fin, String treeFile)
+ throws IOException
+ {
+ // n/a -- already done by standard Jalview command line processing
+ }
+
+ @Override
+ public void setAlignPdbStructures(boolean defaultParameter)
+ {
+ alignPDBStructures = true;
+ }
+
+ @Override
+ public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
+ String[] chains, DataSourceType protocol)
+ {
+ StructureViewer.launchStructureViewer(af.alignPanel, pdb, seqs);
+ }
+
+ @Override
+ public void setFeatureGroupState(String[] groups, boolean state)
+ {
+ af.setFeatureGroupState(groups, state);
+ }
+
+ @Override
+ public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
+ String[][] chains, String[] protocols)
+ {
+ System.err.println(
+ "Jalview applet interface alignedStructureView not implemented");
+ }
+
+ @Override
+ public void newFeatureSettings()
+ {
+ System.err.println(
+ "Jalview applet interface newFeatureSettings not implemented");
+ }
+
+ private Vector<Runnable> jsExecQueue;
+
+ @Override
+ public Vector<Runnable> getJsExecQueue(JSFunctionExec exec)
+ {
+ jsFunctionExec = exec;
+ return (jsExecQueue == null ? (jsExecQueue = new Vector<>())
+ : jsExecQueue);
+ }
+
+ @Override
+ public AppletContext getAppletContext()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public boolean isJsfallbackEnabled()
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public JSObject getJSObject()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public StructureSelectionManagerProvider getStructureSelectionManagerProvider()
+ {
+ // TODO Q: what exactly is this? BH
+ return null;
+ }
+
+ @Override
+ public void updateColoursFromMouseOver(Object source,
+ MouseOverStructureListener mouseOverStructureListener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public Object[] getSelectionForListener(SequenceGroup seqsel,
+ ColumnSelection colsel, HiddenColumns hidden,
+ SelectionSource source, Object alignFrame)
+ {
+ return appLoader.getSelectionForListener(getCurrentAlignFrame(),
+ seqsel, colsel, hidden, source, alignFrame);
+ }
+
+ @Override
+ public String arrayToSeparatorList(String[] array)
+ {
+ return appLoader.arrayToSeparatorList(array);
+ }
+
+ @Override
+ public Hashtable<String, int[]> getJSHashes()
+ {
+ return (jshashes == null ? (jshashes = new Hashtable<>())
+ : jshashes);
+ }
+
+ @Override
+ public Hashtable<String, Hashtable<String, String[]>> getJSMessages()
+ {
+ return (jsmessages == null ? (jsmessages = new Hashtable<>())
+ : jsmessages);
+ }
+
+ @Override
+ public Object getFrameForSource(VamsasSource source)
+ {
+ if (source != null)
+ {
+ AlignFrame af;
+ if (source instanceof jalview.gui.AlignViewport
+ && source == (af = getCurrentAlignFrame()).getViewport())
+ {
+ // should be valid if it just generated an event!
+ return af;
+ }
+ // TODO: ensure that if '_af' is specified along with a handler
+ // function, then only events from that alignFrame are sent to that
+ // function
+ }
+ return null;
+ }
+
+ @Override
+ public FeatureRenderer getNewFeatureRenderer(AlignViewportI vp)
+ {
+ return new jalview.gui.FeatureRenderer((AlignmentPanel) vp);
+ }
+
+ };
+
+ appLoader = new JalviewAppLoader(true);
+ appLoader.load(app);
+ }
+
+ /**
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
+ */
+ @Override
+ public String getSelectedSequences()
{
- return Jalview.currentAlignFrame;
+ return getSelectedSequencesFrom(getCurrentAlignFrame());
}
- public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
+ /**
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
+ */
+ @Override
+ public String getSelectedSequences(String sep)
+ {
+ return getSelectedSequencesFrom(getCurrentAlignFrame(), sep);
+ }
+
+ /**
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+ * .AlignFrame)
+ */
+ @Override
+ public String getSelectedSequencesFrom(AlignFrameI alf)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return getSelectedSequencesFrom(alf, null);
+ }
+
+ /**
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+ * .AlignFrame, java.lang.String)
+ */
+ @Override
+ public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.getSelectedSequencesFrom(alf, sep);
+ }
+
+ /**
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+ * .AlignFrame, java.lang.String)
+ */
+ @Override
+ public void highlight(String sequenceId, String position,
+ String alignedPosition)
+ {
+ highlightIn(null, sequenceId, position,
+ alignedPosition);
+ }
+
+ @Override
+ public void highlightIn(AlignFrameI alf, String sequenceId,
+ String position, String alignedPosition)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ appLoader.highlightIn(alf, sequenceId, position, alignedPosition);
+ }
+
+ @Override
+ public void select(String sequenceIds, String columns)
+ {
+ selectIn(getCurrentAlignFrame(), sequenceIds, columns, null);
+ }
+
+ @Override
+ public void select(String sequenceIds, String columns, String sep)
+ {
+ selectIn(null, sequenceIds, columns, sep);
+ }
+
+ @Override
+ public void selectIn(AlignFrameI alf, String sequenceIds, String columns)
+ {
+ selectIn(alf, sequenceIds, columns, null);
+ }
+
+ @Override
+ public void selectIn(AlignFrameI alf, String sequenceIds, String columns,
+ String sep)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ appLoader.selectIn(alf, sequenceIds, columns, sep);
+ }
+
+ @Override
+ public String getSelectedSequencesAsAlignment(String format,
+ String suffix)
+ {
+ return getSelectedSequencesAsAlignmentFrom(null,
+ format, suffix);
+ }
+
+ @Override
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+ String format, String sep)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep);
+ }
+
+ @Override
+ public String getAlignmentOrder()
+ {
+ return getAlignmentFrom(getCurrentAlignFrame(), null);
+ }
+
+ @Override
+ public String getAlignmentOrderFrom(AlignFrameI alf)
+ {
+ return getAlignmentFrom(alf, null);
+ }
+
+ @Override
+ public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.getAlignmentOrderFrom(alf, sep);
+ }
+
+ @Override
+ public String orderBy(String order, String undoName)
+ {
+ return orderBy(order, undoName, null);
+ }
+
+ @Override
+ public String orderBy(String order, String undoName, String sep)
+ {
+ return orderAlignmentBy(getCurrentAlignFrame(), order, undoName, sep);
+ }
+
+ @Override
+ public String orderAlignmentBy(AlignFrameI alf, String order,
+ String undoName, String sep)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.orderAlignmentBy(alf, order, undoName, sep);
+ }
+
+ @Override
+ public String getAlignment(String format)
+ {
+ return getAlignmentFrom(null, format, null);
+ }
+
+ @Override
+ public String getAlignmentFrom(AlignFrameI alf, String format)
+ {
+ return getAlignmentFrom(alf, format, null);
+ }
+
+ @Override
+ public String getAlignment(String format, String suffix)
+ {
+ return getAlignmentFrom(getCurrentAlignFrame(), format, suffix);
+ }
+
+ @Override
+ public String getAlignmentFrom(AlignFrameI alf, String format,
+ String suffix)
+ {
+ return appLoader.getAlignmentFrom(alf, format, suffix);
+ }
+
+ @Override
+ public void loadAnnotation(String annotation)
+ {
+ loadAnnotationFrom(getCurrentAlignFrame(), annotation);
+ }
+
+ @Override
+ public void loadAnnotationFrom(AlignFrameI alf, String annotation)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ appLoader.loadAnnotationFrom(alf, annotation);
+ }
+
+ @Override
+ public void loadFeatures(String features, boolean autoenabledisplay)
+ {
+ loadFeaturesFrom(currentAlignFrame, features, autoenabledisplay);
+ }
+
+ @Override
+ public boolean loadFeaturesFrom(AlignFrameI alf, String features,
+ boolean autoenabledisplay)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay);
+ }
+
+ @Override
+ public String getFeatures(String format)
+ {
+ return getFeaturesFrom(null, format);
+ }
+
+ @Override
+ public String getFeaturesFrom(AlignFrameI alf, String format)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.getFeaturesFrom(alf, format, true, false);
+ }
+
+ @Override
+ public String getAnnotation()
+ {
+ return getAnnotationFrom(null);
+ }
+
+ @Override
+ public String getAnnotationFrom(AlignFrameI alf)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.getAnnotationFrom(alf);
+ }
+
+ @Override
+ public AlignFrameI newView()
+ {
+ return newViewFrom(null, null);
+ }
+
+ @Override
+ public AlignFrameI newView(String name)
+ {
+ return newViewFrom(null, name);
+ }
+
+ @Override
+ public AlignFrameI newViewFrom(AlignFrameI alf)
+ {
+ return newViewFrom(alf, null);
+ }
+
+ @Override
+ public AlignFrameI newViewFrom(AlignFrameI alf, String name)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.newViewFrom(alf, name);
+ }
+
+ @Override
+ public AlignFrameI loadAlignment(String text, String title)
+ {
+ return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT, title);
+ }
+
+ @Override
+ public boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
+ String pdbEntryString, String pdbFile)
+ {
+ if (alFrame == null)
+ {
+ alFrame = getCurrentAlignFrame();
+ }
+ return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString,
+ pdbFile);
+ }
+
+ @Override
+ public void scrollViewToIn(AlignFrameI alf, String topRow,
+ String leftHandColumn)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ appLoader.scrollViewToIn(alf, topRow, leftHandColumn);
+ }
+
+ @Override
+ public void scrollViewToRowIn(AlignFrameI alf, String topRow)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ appLoader.scrollViewToRowIn(alf, topRow);
+ }
+
+ @Override
+ public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ appLoader.scrollViewToColumnIn(alf, leftHandColumn);
+ }
+
+ @Override
+ public String getFeatureGroups()
+ {
+ return getFeatureGroupsOn(null);
+ }
+
+ @Override
+ public String getFeatureGroupsOn(AlignFrameI alf)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.getFeatureGroupsOn(alf);
+ }
+
+ @Override
+ public String getFeatureGroupsOfState(boolean visible)
+ {
+ return getFeatureGroupsOfStateOn(null, visible);
+ }
+
+ @Override
+ public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.getFeatureGroupsOfStateOn(alf, visible);
+ }
+
+ @Override
+ public void setFeatureGroupState(String groups, boolean state)
+ { // JalviewLite API
+ setFeatureGroupStateOn(null, groups, state);
+ }
+
+ @Override
+ public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
+ boolean state)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ appLoader.setFeatureGroupStateOn(alf, groups, state);
+ }
+
+ @Override
+ public String getSeparator()
{
- Jalview.currentAlignFrame = currentAlignFrame;
+ return appLoader.getSeparator();
}
-}
+
+ @Override
+ public void setSeparator(String separator)
+ {
+ appLoader.setSeparator(separator);
+ }
+
+ @Override
+ public String getJsMessage(String messageclass, String viewId)
+ {
+ // see http://www.jalview.org/examples/jalviewLiteJs.html
+ return null;
+ }
+
+ /**
+ * Open a new Tree panel on the desktop statically. Params are standard (not
+ * set by Groovy). No dialog is opened.
+ *
+ * @param af
+ * @param treeType
+ * @param modelName
+ * @return null, or the string "label.you_need_at_least_n_sequences" if number
+ * of sequences selected is inappropriate
+ */
+ @Override
+ public Object openTreePanel(AlignFrame af, String treeType,
+ String modelName)
+ { // JalviewJS api
+ if (af == null)
+ {
+ af = getCurrentAlignFrame();
+ }
+ return CalculationChooser.openTreePanel(af, treeType, modelName, null);
+ }
+
+ /**
+ * public static method for JalviewJS API to open a PCAPanel without
+ * necessarily using a dialog.
+ *
+ * @param af
+ * @param modelName
+ * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
+ * if number of sequences selected is inappropriate
+ */
+ @Override
+ public Object openPcaPanel(AlignFrame af, String modelName)
+ {
+ if (af == null)
+ {
+ af = getCurrentAlignFrame();
+ }
+ return CalculationChooser.openPcaPanel(af, modelName, null);
+ }
+
+ @Override
+ public String getSelectedSequencesAsAlignment(String format,
+ boolean suffix)
+ {
+ return getSelectedSequencesAsAlignmentFrom(null,
+ format, suffix);
+ }
+
+ @Override
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+ String format, boolean suffix)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format,
+ "" + suffix);
+ }
+
+ @Override
+ public String arrayToSeparatorList(String[] array)
+ {
+ return appLoader.arrayToSeparatorList(array);
+ }
+
+ @Override
+ public String[] separatorListToArray(String list)
+ {
+ return appLoader.separatorListToArray(list);
+ }
+
+ //// probably not needed in JalviewJS -- From when Jmol and Jalview did not
+ //// have a direct connection?
+
+ @Override
+ public void setMouseoverListener(String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setMouseoverListener(AlignFrameI af, String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setSelectionListener(String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setSelectionListener(AlignFrameI af, String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setStructureListener(String listener, String modelSet)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void removeJavascriptListener(AlignFrameI af, String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void mouseOverStructure(String pdbResNum, String chain,
+ String pdbfile)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void showOverview()
+ {
+ currentAlignFrame.overviewMenuItem_actionPerformed(null);
+ }
+
+ public void notifyWorker(AlignCalcWorkerI worker, String status)
+ {
+ // System.out.println("Jalview worker " + worker.getClass().getSimpleName()
+ // + " " + status);
+ }
+
+ /**
+ * flag to allow selected Runnable and Thread processes to run synchronously
+ *
+ * JAL-3563
+ *
+ */
+ private static boolean isSynchronous = false;
+
+ /**
+ * Set Jalview to run selected processes synchronously in test and headless
+ * environments.
+ *
+ * JAL-3563
+ *
+ * @param b
+ * @author Bob Hanson
+ */
+ public static void setSynchronous(boolean b)
+ {
+ isSynchronous = b;
+ }
+
+ /**
+ * Allows optional synchronous running of a Runnable that would otherwise use
+ * SwingUtilities.invokeLater.
+ *
+ * JAL-3563
+ *
+ * @param t
+ * @author Bob Hanson
+ */
+ public static boolean isSynchronous()
+ {
+ return isSynchronous;
+ }
+
+ /**
+ * Allows optional synchronous running of a Runnable that would otherwise use
+ * SwingUtilities.invokeLater.
+ *
+ * JAL-3563
+ *
+ * @param t
+ * @author Bob Hanson
+ */
+ public static void execRunnable(Runnable r)
+ {
+ if (isSynchronous())
+ {
+ r.run();
+ }
+ else
+ {
+ SwingUtilities.invokeLater(r);
+ }
+ }
+
+ /**
+ * Allows optional synchronous running of a thread that would otherwise be run
+ * using start().
+ *
+ * JAL-3563
+ *
+ * @param t
+ * @author Bob Hanson
+ */
+ public static void execThread(Thread t)
+ {
+ if (isSynchronous())
+ {
+ t.run();
+ }
+ else
+ {
+ t.start();
+ }
+ }
+
+ /**
+ * Get the SwingJS applet ID and combine that with the frameType
+ *
+ * @param frameType
+ * "alignment", "desktop", etc., or null
+ * @return
+ */
+ public static String getAppID(String frameType)
+ {
+ String id = Cache.getProperty("Info.j2sAppletID");
+ if (id == null)
+ {
+ id = "jalview";
+ }
+ return id + (frameType == null ? "" : "-" + frameType);
+ }
+
+}
\ No newline at end of file
--- /dev/null
+package jalview.bin;
+
+import jalview.api.AlignFrameI;
+import jalview.api.JalviewApp;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.Desktop;
+import jalview.io.AnnotationFile;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FeaturesFile;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
+import jalview.io.IdentifyFile;
+import jalview.io.JPredFile;
+import jalview.io.JnetAnnotationMaker;
+import jalview.io.NewickFile;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.HttpUtils;
+import jalview.util.MessageManager;
+
+import java.io.IOException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+/**
+ * A class to load parameters for either JalviewLite or Jalview
+ *
+ * @author hansonr
+ *
+ */
+public class JalviewAppLoader
+{
+
+ private JalviewApp app; // Jalview or JalviewJS or JalviewLite
+
+ private boolean debug;
+
+ String separator = "\u00AC"; // JalviewLite note: the default used to
+ // be '|', but many sequence IDS include
+ // pipes.
+
+ public String getSeparator()
+ {
+ return separator;
+ }
+
+ public void setSeparator(String separator)
+ {
+ this.separator = separator;
+ }
+
+ public JalviewAppLoader(boolean debug)
+ {
+ this.debug = debug;
+ }
+
+ public void load(JalviewApp app)
+ {
+
+ this.app = app;
+
+ String sep = app.getParameter("separator");
+ if (sep != null)
+ {
+ if (sep.length() > 0)
+ {
+ separator = sep;
+ }
+ else
+ {
+ throw new Error(MessageManager
+ .getString("error.invalid_separator_parameter"));
+ }
+ }
+
+ loadTree();
+ loadScoreFile();
+ loadFeatures();
+ loadAnnotations();
+ loadJnetFile();
+ loadPdbFiles();
+ callInitCallback();
+ }
+
+ /**
+ * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
+ * else false.
+ *
+ * @param loaderFrame
+ * @return
+ */
+ protected boolean loadPdbFiles()
+ {
+ boolean result = false;
+ /*
+ * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 -
+ * related to JAL-434
+ */
+
+ boolean doAlign = app.getDefaultParameter("alignpdbfiles", false);
+ app.setAlignPdbStructures(doAlign);
+ /*
+ * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
+ * PDB|1GAQ|1GAQ|C">
+ *
+ * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
+ *
+ * <param name="PDBfile3" value="1q0o Q45135_9MICO">
+ */
+
+ // Accumulate pdbs here if they are heading for the same view (if
+ // alignPdbStructures is true)
+ Vector<Object[]> pdbs = new Vector<>();
+ // create a lazy matcher if we're asked to
+ jalview.analysis.SequenceIdMatcher matcher = (app
+ .getDefaultParameter("relaxedidmatch", false))
+ ? new jalview.analysis.SequenceIdMatcher(
+ app.getViewport().getAlignment()
+ .getSequencesArray())
+ : null;
+
+ int pdbFileCount = 0;
+ String param;
+ do
+ {
+ if (pdbFileCount > 0)
+ {
+ param = app.getParameter("PDBFILE" + pdbFileCount);
+ }
+ else
+ {
+ param = app.getParameter("PDBFILE");
+ }
+
+ if (param != null)
+ {
+ PDBEntry pdb = new PDBEntry();
+
+ String seqstring;
+ SequenceI[] seqs = null;
+ String[] chains = null;
+
+ StringTokenizer st = new StringTokenizer(param, " ");
+
+ if (st.countTokens() < 2)
+ {
+ String sequence = app.getParameter("PDBSEQ");
+ if (sequence != null)
+ {
+ seqs = new SequenceI[] { matcher == null
+ ? (Sequence) app.getViewport().getAlignment()
+ .findName(sequence)
+ : matcher.findIdMatch(sequence) };
+ }
+
+ }
+ else
+ {
+ param = st.nextToken();
+ List<SequenceI> tmp = new ArrayList<>();
+ List<String> tmp2 = new ArrayList<>();
+
+ while (st.hasMoreTokens())
+ {
+ seqstring = st.nextToken();
+ StringTokenizer st2 = new StringTokenizer(seqstring, "=");
+ if (st2.countTokens() > 1)
+ {
+ // This is the chain
+ tmp2.add(st2.nextToken());
+ seqstring = st2.nextToken();
+ }
+ tmp.add(matcher == null
+ ? (Sequence) app.getViewport().getAlignment()
+ .findName(seqstring)
+ : matcher.findIdMatch(seqstring));
+ }
+
+ seqs = tmp.toArray(new SequenceI[tmp.size()]);
+ if (tmp2.size() == tmp.size())
+ {
+ chains = tmp2.toArray(new String[tmp2.size()]);
+ }
+ }
+ pdb.setId(param);
+ ret[0] = param;
+ DataSourceType protocol = resolveFileProtocol(app, ret);
+ // TODO check JAL-357 for files in a jar (CLASSLOADER)
+ pdb.setFile(ret[0]);
+
+ if (seqs != null)
+ {
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (seqs[i] != null)
+ {
+ ((Sequence) seqs[i]).addPDBId(pdb);
+ StructureSelectionManager
+ .getStructureSelectionManager(
+ (StructureSelectionManagerProvider) app)
+ .registerPDBEntry(pdb);
+ }
+ else
+ {
+ if (debug)
+ {
+ // this may not really be a problem but we give a warning
+ // anyway
+ System.err.println(
+ "Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
+ + i + ")");
+ }
+ }
+ }
+
+ if (doAlign)
+ {
+ pdbs.addElement(new Object[] { pdb, seqs, chains, protocol });
+ }
+ else
+ {
+ app.newStructureView(pdb, seqs, chains, protocol);
+ }
+ }
+ }
+
+ pdbFileCount++;
+ } while (param != null || pdbFileCount < 10);
+ if (pdbs.size() > 0)
+ {
+ SequenceI[][] seqs = new SequenceI[pdbs.size()][];
+ PDBEntry[] pdb = new PDBEntry[pdbs.size()];
+ String[][] chains = new String[pdbs.size()][];
+ String[] protocols = new String[pdbs.size()];
+ for (int pdbsi = 0, pdbsiSize = pdbs
+ .size(); pdbsi < pdbsiSize; pdbsi++)
+ {
+ Object[] o = pdbs.elementAt(pdbsi);
+ pdb[pdbsi] = (PDBEntry) o[0];
+ seqs[pdbsi] = (SequenceI[]) o[1];
+ chains[pdbsi] = (String[]) o[2];
+ protocols[pdbsi] = (String) o[3];
+ }
+ app.alignedStructureView(pdb, seqs, chains, protocols);
+ result = true;
+ }
+ return result;
+ }
+
+ /**
+ * Load in a Jnetfile if specified by parameter. Returns true if loaded, else
+ * false.
+ *
+ * @param alignFrame
+ * @return
+ */
+ protected boolean loadJnetFile()
+ {
+ boolean result = false;
+ String param = app.getParameter("jnetfile");
+ if (param == null)
+ {
+ // jnet became jpred around 2016
+ param = app.getParameter("jpredfile");
+ }
+ if (param != null)
+ {
+ try
+ {
+ ret[0] = param;
+ DataSourceType protocol = resolveFileProtocol(app, ret);
+ JPredFile predictions = new JPredFile(ret[0], protocol);
+ JnetAnnotationMaker.add_annotation(predictions,
+ app.getViewport().getAlignment(), 0, false);
+ // false == do not add sequence profile from concise output
+ app.getViewport().getAlignment().setupJPredAlignment();
+ app.updateForAnnotations();
+ result = true;
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Load annotations if specified by parameter. Returns true if loaded, else
+ * false.
+ *
+ * @param alignFrame
+ * @return
+ */
+ protected boolean loadAnnotations()
+ {
+ boolean result = false;
+ String param = app.getParameter("annotations");
+ if (param != null)
+ {
+ ret[0] = param;
+ DataSourceType protocol = resolveFileProtocol(app, ret);
+ param = ret[0];
+ if (new AnnotationFile().annotateAlignmentView(app.getViewport(),
+ param, protocol))
+ {
+ app.updateForAnnotations();
+ result = true;
+ }
+ else
+ {
+ System.err
+ .println("Annotations were not added from annotation file '"
+ + param + "'");
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Load features file and view settings as specified by parameters. Returns
+ * true if features were loaded, else false.
+ *
+ * @param alignFrame
+ * @return
+ */
+ protected boolean loadFeatures()
+ {
+ boolean result = false;
+ // ///////////////////////////
+ // modify display of features
+ // we do this before any features have been loaded, ensuring any hidden
+ // groups are hidden when features first displayed
+ //
+ // hide specific groups
+ //
+ String param = app.getParameter("hidefeaturegroups");
+ if (param != null)
+ {
+ app.setFeatureGroupState(separatorListToArray(param, separator),
+ false);
+ // app.setFeatureGroupStateOn(newAlignFrame, param, false);
+ }
+ // show specific groups
+ param = app.getParameter("showfeaturegroups");
+ if (param != null)
+ {
+ app.setFeatureGroupState(separatorListToArray(param, separator),
+ true);
+ // app.setFeatureGroupStateOn(newAlignFrame, param, true);
+ }
+ // and now load features
+ param = app.getParameter("features");
+ if (param != null)
+ {
+ ret[0] = param;
+ DataSourceType protocol = resolveFileProtocol(app, ret);
+
+ result = app.parseFeaturesFile(ret[0], protocol);
+ }
+
+ param = app.getParameter("showFeatureSettings");
+ if (param != null && param.equalsIgnoreCase("true"))
+ {
+ app.newFeatureSettings();
+ }
+ return result;
+ }
+
+ /**
+ * Load a score file if specified by parameter. Returns true if file was
+ * loaded, else false.
+ *
+ * @param loaderFrame
+ */
+ protected boolean loadScoreFile()
+ {
+ boolean result = false;
+ String sScoreFile = app.getParameter("scoreFile");
+ if (sScoreFile != null && !"".equals(sScoreFile))
+ {
+ try
+ {
+ if (debug)
+ {
+ System.err.println(
+ "Attempting to load T-COFFEE score file from the scoreFile parameter");
+ }
+ result = app.loadScoreFile(sScoreFile);
+ if (!result)
+ {
+ System.err.println(
+ "Failed to parse T-COFFEE parameter as a valid score file ('"
+ + sScoreFile + "')");
+ }
+ } catch (Exception e)
+ {
+ System.err.printf("Cannot read score file: '%s'. Cause: %s \n",
+ sScoreFile, e.getMessage());
+ }
+ }
+ return result;
+ }
+
+ String[] ret = new String[1];
+
+ /**
+ * Load a tree for the alignment if specified by parameter. Returns true if a
+ * tree was loaded, else false.
+ *
+ * @param loaderFrame
+ * @return
+ */
+ protected boolean loadTree()
+ {
+ boolean result = false;
+ String treeFile = app.getParameter("tree");
+ if (treeFile == null)
+ {
+ treeFile = app.getParameter("treeFile");
+ }
+
+ if (treeFile != null)
+ {
+ try
+ {
+ ret[0] = treeFile;
+ NewickFile fin = new NewickFile(treeFile,
+ resolveFileProtocol(app, ret));
+ fin.parse();
+
+ if (fin.getTree() != null)
+ {
+ app.loadTree(fin, ret[0]);
+ result = true;
+ if (debug)
+ {
+ System.out.println("Successfully imported tree.");
+ }
+ }
+ else
+ {
+ if (debug)
+ {
+ System.out.println(
+ "Tree parameter did not resolve to a valid tree.");
+ }
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ return result;
+ }
+
+ /**
+ * form a complete URL given a path to a resource and a reference location on
+ * the same server
+ *
+ * @param targetPath
+ * - an absolute path on the same server as localref or a document
+ * located relative to localref
+ * @param localref
+ * - a URL on the same server as url
+ * @return a complete URL for the resource located by url
+ */
+ public static String resolveUrlForLocalOrAbsolute(String targetPath,
+ URL localref)
+ {
+ String resolvedPath = "";
+ if (targetPath.startsWith("/"))
+ {
+ String codebase = localref.toString();
+ String localfile = localref.getFile();
+ resolvedPath = codebase.substring(0,
+ codebase.length() - localfile.length()) + targetPath;
+ return resolvedPath;
+ }
+
+ /*
+ * get URL path and strip off any trailing file e.g.
+ * www.jalview.org/examples/index.html#applets?a=b is trimmed to
+ * www.jalview.org/examples/
+ */
+ String urlPath = localref.toString();
+ String directoryPath = urlPath;
+ int lastSeparator = directoryPath.lastIndexOf("/");
+ if (lastSeparator > 0)
+ {
+ directoryPath = directoryPath.substring(0, lastSeparator + 1);
+ }
+
+ if (targetPath.startsWith("/"))
+ {
+ /*
+ * construct absolute URL to a file on the server - this is not allowed?
+ */
+ // String localfile = localref.getFile();
+ // resolvedPath = urlPath.substring(0,
+ // urlPath.length() - localfile.length())
+ // + targetPath;
+ resolvedPath = directoryPath + targetPath.substring(1);
+ }
+ else
+ {
+ resolvedPath = directoryPath + targetPath;
+ }
+ // if (debug)
+ // {
+ // System.err.println(
+ // "resolveUrlForLocalOrAbsolute returning " + resolvedPath);
+ // }
+ return resolvedPath;
+ }
+
+ /**
+ * parse the string into a list
+ *
+ * @param list
+ * @param separator
+ * @return elements separated by separator
+ */
+ public static String[] separatorListToArray(String list, String separator)
+ {
+ // TODO use StringUtils version (slightly different...)
+ int seplen = separator.length();
+ if (list == null || list.equals("") || list.equals(separator))
+ {
+ return null;
+ }
+ Vector<String> jv = new Vector<>();
+ int cp = 0, pos;
+ while ((pos = list.indexOf(separator, cp)) > cp)
+ {
+ jv.addElement(list.substring(cp, pos));
+ cp = pos + seplen;
+ }
+ if (cp < list.length())
+ {
+ String c = list.substring(cp);
+ if (!c.equals(separator))
+ {
+ jv.addElement(c);
+ }
+ }
+ if (jv.size() > 0)
+ {
+ String[] v = new String[jv.size()];
+ for (int i = 0; i < v.length; i++)
+ {
+ v[i] = jv.elementAt(i);
+ }
+ jv.removeAllElements();
+ // if (debug)
+ // {
+ // System.err.println("Array from '" + separator
+ // + "' separated List:\n" + v.length);
+ // for (int i = 0; i < v.length; i++)
+ // {
+ // System.err.println("item " + i + " '" + v[i] + "'");
+ // }
+ // }
+ return v;
+ }
+ // if (debug)
+ // {
+ // System.err.println(
+ // "Empty Array from '" + separator + "' separated List");
+ // }
+ return null;
+ }
+
+ public static DataSourceType resolveFileProtocol(JalviewApp app,
+ String[] retPath)
+ {
+ String path = retPath[0];
+ /*
+ * is it paste data?
+ */
+ if (path.startsWith("PASTE"))
+ {
+ retPath[0] = path.substring(5);
+ return DataSourceType.PASTE;
+ }
+
+ /*
+ * is it a URL?
+ */
+ if (path.indexOf("://") >= 0)
+ {
+ return DataSourceType.URL;
+ }
+
+ /*
+ * try relative to document root
+ */
+ URL documentBase = app.getDocumentBase();
+ String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase);
+ if (HttpUtils.isValidUrl(withDocBase))
+ {
+ // if (debug)
+ // {
+ // System.err.println("Prepended document base '" + documentBase
+ // + "' to make: '" + withDocBase + "'");
+ // }
+ retPath[0] = withDocBase;
+ return DataSourceType.URL;
+ }
+
+ /*
+ * try relative to codebase (if different to document base)
+ */
+ URL codeBase = app.getCodeBase();
+ String withCodeBase = resolveUrlForLocalOrAbsolute(path, codeBase);
+ if (!withCodeBase.equals(withDocBase)
+ && HttpUtils.isValidUrl(withCodeBase))
+ {
+ // if (debug)
+ // {
+ // System.err.println("Prepended codebase '" + codeBase
+ // + "' to make: '" + withCodeBase + "'");
+ // }
+ retPath[0] = withCodeBase;
+ return DataSourceType.URL;
+ }
+
+ /*
+ * try locating by classloader; try this last so files in the directory
+ * are resolved using document base
+ */
+ if (inArchive(app.getClass(), path))
+ {
+ return DataSourceType.CLASSLOADER;
+ }
+ return null;
+ }
+
+ /**
+ * Discovers whether the given file is in the Applet Archive
+ *
+ * @param f
+ * String
+ * @return boolean
+ */
+ private static boolean inArchive(Class<?> c, String f)
+ {
+ // This might throw a security exception in certain browsers
+ // Netscape Communicator for instance.
+ try
+ {
+ boolean rtn = (c.getResourceAsStream("/" + f) != null);
+ // if (debug)
+ // {
+ // System.err.println("Resource '" + f + "' was "
+ // + (rtn ? "" : "not ") + "located by classloader.");
+ // }
+ return rtn;
+ } catch (Exception ex)
+ {
+ System.out.println("Exception checking resources: " + f + " " + ex);
+ return false;
+ }
+ }
+
+ public void callInitCallback()
+ {
+ String initjscallback = app.getParameter("oninit");
+ if (initjscallback == null)
+ {
+ return;
+ }
+ initjscallback = initjscallback.trim();
+ if (initjscallback.length() > 0)
+ {
+ // TODO
+ }
+ }
+
+ /**
+ * read sequence1...sequenceN as a raw alignment
+ *
+ * @param jalviewApp
+ * @return
+ */
+ public String getPastedSequence(JalviewApp jalviewApp)
+ {
+ StringBuffer data = new StringBuffer("PASTE");
+ int i = 1;
+ String file = null;
+ while ((file = app.getParameter("sequence" + i)) != null)
+ {
+ data.append(file.toString() + "\n");
+ i++;
+ }
+ if (data.length() > 5)
+ {
+ file = data.toString();
+ }
+ return file;
+ }
+
+ /**
+ * concatenate the list with separator
+ *
+ * @param list
+ * @param separator
+ * @return concatenated string
+ */
+ public static String arrayToSeparatorList(String[] list, String separator)
+ {
+ // TODO use StringUtils version
+ StringBuffer v = new StringBuffer();
+ if (list != null && list.length > 0)
+ {
+ for (int i = 0, iSize = list.length; i < iSize; i++)
+ {
+ if (list[i] != null)
+ {
+ if (i > 0)
+ {
+ v.append(separator);
+ }
+ v.append(list[i]);
+ }
+ }
+ // if (debug)
+ // {
+ // System.err
+ // .println("Returning '" + separator + "' separated List:\n");
+ // System.err.println(v);
+ // }
+ return v.toString();
+ }
+ // if (debug)
+ // {
+ // System.err.println(
+ // "Returning empty '" + separator + "' separated List\n");
+ // }
+ return "" + separator;
+ }
+
+ public String arrayToSeparatorList(String[] array)
+ {
+ return arrayToSeparatorList(array, separator);
+ }
+
+ public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
+ {
+ StringBuffer result = new StringBuffer("");
+ if (sep == null || sep.length() == 0)
+ {
+ sep = separator; // "+0x00AC;
+ }
+ AlignViewport v = ((AlignFrame) alf).getViewport();
+ if (v.getSelectionGroup() != null)
+ {
+ SequenceI[] seqs = v.getSelectionGroup()
+ .getSequencesInOrder(v.getAlignment());
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ result.append(seqs[i].getName());
+ result.append(sep);
+ }
+ }
+
+ return result.toString();
+ }
+
+ public void setFeatureGroupStateOn(final AlignFrameI alf,
+ final String groups, boolean state)
+ {
+ Jalview.execRunnable(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ ((AlignFrame) alf).setFeatureGroupState(
+ separatorListToArray(groups, separator), state);
+ }
+ });
+ }
+
+ public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
+ {
+ return arrayToSeparatorList(
+ ((AlignFrame) alf).getFeatureGroupsOfState(visible));
+ }
+
+ public void scrollViewToIn(final AlignFrameI alf, final String topRow,
+ final String leftHandColumn)
+ {
+ Jalview.execRunnable(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ ((AlignFrame) alf).scrollTo(new Integer(topRow).intValue(),
+ new Integer(leftHandColumn).intValue());
+
+ } catch (Exception ex)
+ {
+ System.err.println("Couldn't parse integer arguments (topRow='"
+ + topRow + "' and leftHandColumn='" + leftHandColumn
+ + "')");
+ ex.printStackTrace();
+ }
+ }
+ });
+ }
+
+ public void scrollViewToRowIn(final AlignFrameI alf, final String topRow)
+ {
+
+ Jalview.execRunnable(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ ((AlignFrame) alf).scrollToRow(new Integer(topRow).intValue());
+
+ } catch (Exception ex)
+ {
+ System.err.println("Couldn't parse integer arguments (topRow='"
+ + topRow + "')");
+ ex.printStackTrace();
+ }
+
+ }
+ });
+ }
+
+ public void scrollViewToColumnIn(final AlignFrameI alf,
+ final String leftHandColumn)
+ {
+ Jalview.execRunnable(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ ((AlignFrame) alf)
+ .scrollToColumn(new Integer(leftHandColumn).intValue());
+
+ } catch (Exception ex)
+ {
+ System.err.println(
+ "Couldn't parse integer arguments (leftHandColumn='"
+ + leftHandColumn + "')");
+ ex.printStackTrace();
+ }
+ }
+ });
+
+ }
+
+ public boolean addPdbFile(AlignFrameI alf, String sequenceId,
+ String pdbEntryString, String pdbFile)
+ {
+ AlignFrame alFrame = (AlignFrame) alf;
+ SequenceI toaddpdb = alFrame.getViewport().getAlignment()
+ .findName(sequenceId);
+ boolean needtoadd = false;
+ if (toaddpdb != null)
+ {
+ Vector<PDBEntry> pdbe = toaddpdb.getAllPDBEntries();
+ PDBEntry pdbentry = null;
+ if (pdbe != null && pdbe.size() > 0)
+ {
+ for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
+ {
+ pdbentry = pdbe.elementAt(pe);
+ if (!pdbentry.getId().equals(pdbEntryString)
+ && !pdbentry.getFile().equals(pdbFile))
+ {
+ pdbentry = null;
+ }
+ else
+ {
+ continue;
+ }
+ }
+ }
+ if (pdbentry == null)
+ {
+ pdbentry = new PDBEntry();
+ pdbentry.setId(pdbEntryString);
+ pdbentry.setFile(pdbFile);
+ needtoadd = true; // add this new entry to sequence.
+ }
+ // resolve data source
+ // TODO: this code should be a refactored to an io package
+ DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
+ FileFormat.PDB);
+ if (protocol == null)
+ {
+ return false;
+ }
+ if (needtoadd)
+ {
+ pdbentry.setProperty("protocol", protocol);
+ toaddpdb.addPDBId(pdbentry);
+ alFrame.alignPanel.getStructureSelectionManager()
+ .registerPDBEntry(pdbentry);
+ }
+ }
+ return true;
+ }
+
+ public AlignFrameI loadAlignment(String text, int width, int height,
+ String title)
+ {
+ AlignmentI al = null;
+
+ try
+ {
+ FileFormatI format = new IdentifyFile().identify(text,
+ DataSourceType.PASTE);
+ al = new AppletFormatAdapter().readFile(text, DataSourceType.PASTE,
+ format);
+ if (al.getHeight() > 0)
+ {
+ return new AlignFrame(al, width, height, title);
+ }
+ } catch (IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ return null;
+ }
+
+ public String getFeatureGroupsOn(AlignFrameI alf)
+ {
+ return arrayToSeparatorList(
+ ((AlignFrame) alf).getFeatureGroups());
+ }
+
+ public void highlightIn(final AlignFrameI alf, final String sequenceId,
+ final String position, final String alignedPosition)
+ {
+ // TODO: could try to highlight in all alignments if alf==null
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ ((AlignFrame) alf).getViewport().getAlignment()
+ .getSequencesArray());
+ final SequenceI sq = matcher.findIdMatch(sequenceId);
+ if (sq != null)
+ {
+ int apos = -1;
+ try
+ {
+ apos = new Integer(position).intValue();
+ apos--;
+ } catch (NumberFormatException ex)
+ {
+ return;
+ }
+ final int pos = apos;
+ // use vamsas listener to broadcast to all listeners in scope
+ if (alignedPosition != null && (alignedPosition.trim().length() == 0
+ || alignedPosition.toLowerCase().indexOf("false") > -1))
+ {
+ Jalview.execRunnable(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ StructureSelectionManager
+ .getStructureSelectionManager(Desktop.getInstance())
+ .mouseOverVamsasSequence(sq, sq.findIndex(pos), null);
+ }
+ });
+ }
+ else
+ {
+ Jalview.execRunnable(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ StructureSelectionManager
+ .getStructureSelectionManager(Desktop.getInstance())
+ .mouseOverVamsasSequence(sq, pos, null);
+ }
+ });
+ }
+ }
+ }
+
+ public void selectIn(final AlignFrameI alf, String sequenceIds,
+ String columns, String sep)
+ {
+ if (sep == null || sep.length() == 0)
+ {
+ sep = separator;
+ }
+ else
+ {
+ if (debug)
+ {
+ System.err.println("Selecting region using separator string '"
+ + separator + "'");
+ }
+ }
+ // deparse fields
+ String[] ids = JalviewAppLoader.separatorListToArray(sequenceIds, sep);
+ String[] cols = JalviewAppLoader.separatorListToArray(columns, sep);
+ final SequenceGroup sel = new SequenceGroup();
+ final ColumnSelection csel = new ColumnSelection();
+ AlignmentI al = ((AlignFrame) alf).getViewport().getAlignment();
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ ((AlignFrame) alf).getViewport().getAlignment()
+ .getSequencesArray());
+ int start = 0, end = al.getWidth(), alw = al.getWidth();
+ boolean seqsfound = true;
+ if (ids != null && ids.length > 0)
+ {
+ seqsfound = false;
+ for (int i = 0; i < ids.length; i++)
+ {
+ if (ids[i].trim().length() == 0)
+ {
+ continue;
+ }
+ SequenceI sq = matcher.findIdMatch(ids[i]);
+ if (sq != null)
+ {
+ seqsfound = true;
+ sel.addSequence(sq, false);
+ }
+ }
+ }
+ boolean inseqpos = false;
+ if (cols != null && cols.length > 0)
+ {
+ boolean seset = false;
+ for (int i = 0; i < cols.length; i++)
+ {
+ String cl = cols[i].trim();
+ if (cl.length() == 0)
+ {
+ continue;
+ }
+ int p;
+ if ((p = cl.indexOf("-")) > -1)
+ {
+ int from = -1, to = -1;
+ try
+ {
+ from = new Integer(cl.substring(0, p)).intValue();
+ from--;
+ } catch (NumberFormatException ex)
+ {
+ System.err.println(
+ "ERROR: Couldn't parse first integer in range element column selection string '"
+ + cl + "' - format is 'from-to'");
+ return;
+ }
+ try
+ {
+ to = new Integer(cl.substring(p + 1)).intValue();
+ to--;
+ } catch (NumberFormatException ex)
+ {
+ System.err.println(
+ "ERROR: Couldn't parse second integer in range element column selection string '"
+ + cl + "' - format is 'from-to'");
+ return;
+ }
+ if (from >= 0 && to >= 0)
+ {
+ // valid range
+ if (from < to)
+ {
+ int t = to;
+ to = from;
+ to = t;
+ }
+ if (!seset)
+ {
+ start = from;
+ end = to;
+ seset = true;
+ }
+ else
+ {
+ // comment to prevent range extension
+ if (start > from)
+ {
+ start = from;
+ }
+ if (end < to)
+ {
+ end = to;
+ }
+ }
+ for (int r = from; r <= to; r++)
+ {
+ if (r >= 0 && r < alw)
+ {
+ csel.addElement(r);
+ }
+ }
+ if (debug)
+ {
+ System.err.println("Range '" + cl + "' deparsed as [" + from
+ + "," + to + "]");
+ }
+ }
+ else
+ {
+ System.err.println("ERROR: Invalid Range '" + cl
+ + "' deparsed as [" + from + "," + to + "]");
+ }
+ }
+ else
+ {
+ int r = -1;
+ try
+ {
+ r = new Integer(cl).intValue();
+ r--;
+ } catch (NumberFormatException ex)
+ {
+ if (cl.toLowerCase().equals("sequence"))
+ {
+ // we are in the dataset sequence's coordinate frame.
+ inseqpos = true;
+ }
+ else
+ {
+ System.err.println(
+ "ERROR: Couldn't parse integer from point selection element of column selection string '"
+ + cl + "'");
+ return;
+ }
+ }
+ if (r >= 0 && r <= alw)
+ {
+ if (!seset)
+ {
+ start = r;
+ end = r;
+ seset = true;
+ }
+ else
+ {
+ // comment to prevent range extension
+ if (start > r)
+ {
+ start = r;
+ }
+ if (end < r)
+ {
+ end = r;
+ }
+ }
+ csel.addElement(r);
+ if (debug)
+ {
+ System.err.println("Point selection '" + cl
+ + "' deparsed as [" + r + "]");
+ }
+ }
+ else
+ {
+ System.err.println("ERROR: Invalid Point selection '" + cl
+ + "' deparsed as [" + r + "]");
+ }
+ }
+ }
+ }
+ if (seqsfound)
+ {
+ // we only propagate the selection when it was the null selection, or the
+ // given sequences were found in the alignment.
+ if (inseqpos && sel.getSize() > 0)
+ {
+ // assume first sequence provides reference frame ?
+ SequenceI rs = sel.getSequenceAt(0);
+ start = rs.findIndex(start);
+ end = rs.findIndex(end);
+ List<Integer> cs = new ArrayList<>(csel.getSelected());
+ csel.clear();
+ for (Integer selectedCol : cs)
+ {
+ csel.addElement(rs.findIndex(selectedCol));
+ }
+ }
+ sel.setStartRes(start);
+ sel.setEndRes(end);
+ Jalview.execRunnable(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ ((AlignFrame) alf).select(sel, csel, ((AlignFrame) alf)
+ .getCurrentView().getAlignment().getHiddenColumns());
+ }
+ });
+ }
+ }
+
+ public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
+ {
+ AlignmentI alorder = ((AlignFrame) alf).getViewport().getAlignment();
+ String[] order = new String[alorder.getHeight()];
+ for (int i = 0; i < order.length; i++)
+ {
+ order[i] = alorder.getSequenceAt(i).getName();
+ }
+ return arrayToSeparatorList(order, sep);
+ }
+
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+ String format, String suffix)
+ {
+ try
+ {
+ AlignViewport vp = ((AlignFrame) alf).getViewport();
+ FileFormatI theFormat = FileFormats.getInstance().forName(format);
+ boolean seqlimits = (suffix == null
+ || suffix.equalsIgnoreCase("true"));
+ if (vp.getSelectionGroup() != null)
+ {
+ // JBPNote: getSelectionAsNewSequence behaviour has changed - this
+ // method now returns a full copy of sequence data
+ // TODO consider using getSequenceSelection instead here
+ String reply = new AppletFormatAdapter().formatSequences(theFormat,
+ new Alignment(vp.getSelectionAsNewSequence()),
+ seqlimits);
+ return reply;
+ }
+ } catch (IllegalArgumentException ex)
+ {
+ ex.printStackTrace();
+ return "Error retrieving alignment, possibly invalid format specifier: "
+ + format;
+ }
+ return "";
+ }
+
+ public String orderAlignmentBy(AlignFrameI alf, String order,
+ String undoName, String sep)
+ {
+ if (sep == null || sep.length() == 0)
+ {
+ sep = separator;
+ }
+ String[] ids = JalviewAppLoader.separatorListToArray(order, sep);
+ SequenceI[] sqs = null;
+ if (ids != null && ids.length > 0)
+ {
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ ((AlignFrame) alf).getViewport().getAlignment()
+ .getSequencesArray());
+ int s = 0;
+ sqs = new SequenceI[ids.length];
+ for (int i = 0; i < ids.length; i++)
+ {
+ if (ids[i].trim().length() == 0)
+ {
+ continue;
+ }
+ SequenceI sq = matcher.findIdMatch(ids[i]);
+ if (sq != null)
+ {
+ sqs[s++] = sq;
+ }
+ }
+ if (s > 0)
+ {
+ SequenceI[] sqq = new SequenceI[s];
+ System.arraycopy(sqs, 0, sqq, 0, s);
+ sqs = sqq;
+ }
+ else
+ {
+ sqs = null;
+ }
+ }
+ if (sqs == null)
+ {
+ return "";
+ }
+ final AlignmentOrder aorder = new AlignmentOrder(sqs);
+
+ if (undoName != null && undoName.trim().length() == 0)
+ {
+ undoName = null;
+ }
+ final String _undoName = undoName;
+ // TODO: deal with synchronization here: cannot raise any events until after
+ // this has returned.
+ return ((AlignFrame) alf).sortBy(aorder, _undoName) ? "true" : "";
+ }
+
+ public String getAlignmentFrom(AlignFrameI alf, String format,
+ String suffix)
+ {
+ try
+ {
+ boolean seqlimits = (suffix == null
+ || suffix.equalsIgnoreCase("true"));
+
+ FileFormatI theFormat = FileFormats.getInstance().forName(format);
+ String reply = new AppletFormatAdapter().formatSequences(theFormat,
+ ((AlignFrame) alf).getViewport().getAlignment(), seqlimits);
+ return reply;
+ } catch (IllegalArgumentException ex)
+ {
+ ex.printStackTrace();
+ return "Error retrieving alignment, possibly invalid format specifier: "
+ + format;
+ }
+ }
+
+ public void loadAnnotationFrom(AlignFrameI alf, String annotation)
+ {
+ if (new AnnotationFile().annotateAlignmentView(
+ ((AlignFrame) alf).getViewport(), annotation,
+ DataSourceType.PASTE))
+ {
+ ((AlignFrame) alf).alignPanel.fontChanged();
+ ((AlignFrame) alf).alignPanel.setScrollValues(0, 0);
+ }
+ else
+ {
+ ((AlignFrame) alf).parseFeaturesFile(annotation,
+ DataSourceType.PASTE);
+ }
+ }
+
+ public boolean loadFeaturesFrom(AlignFrameI alf, String features,
+ boolean autoenabledisplay)
+ {
+ boolean ret = ((AlignFrame) alf).parseFeaturesFile(features,
+ DataSourceType.PASTE);
+ if (!ret)
+ {
+ return false;
+ }
+ if (autoenabledisplay)
+ {
+ ((AlignFrame) alf).getViewport().setShowSequenceFeatures(true);
+ // this next was for a checkbox in JalviewLite
+ // ((AlignFrame) alf).getViewport().sequenceFeatures.setState(true);
+ }
+ return true;
+ }
+
+ public String getFeaturesFrom(AlignFrameI alf, String format,
+ boolean includeNonpositionsFeatures, boolean includeComplement)
+ {
+ AlignFrame f = ((AlignFrame) alf);
+
+ String features;
+ FeaturesFile formatter = new FeaturesFile();
+ if (format.equalsIgnoreCase("Jalview"))
+ {
+ features = formatter.printJalviewFormat(
+ f.getViewport().getAlignment().getSequencesArray(),
+ f.alignPanel.getFeatureRenderer(),
+ includeNonpositionsFeatures, includeComplement);
+ }
+ else
+ {
+ features = formatter.printGffFormat(
+ f.getViewport().getAlignment().getSequencesArray(),
+ f.alignPanel.getFeatureRenderer(),
+ includeNonpositionsFeatures, includeComplement);
+ }
+
+ if (features == null)
+ {
+ features = "";
+ }
+ return features;
+
+ }
+
+ public String getAnnotationFrom(AlignFrameI alf)
+ {
+ AlignFrame f = (AlignFrame) alf;
+ String annotation = new AnnotationFile()
+ .printAnnotationsForView(f.getViewport());
+ return annotation;
+ }
+
+ public AlignFrameI newViewFrom(AlignFrameI alf, String name)
+ {
+ return (AlignFrameI) ((AlignFrame) alf).newView(name, true);
+ }
+
+ public String[] separatorListToArray(String list)
+ {
+ return separatorListToArray(list, separator);
+ }
+
+ public Object[] getSelectionForListener(AlignFrameI currentFrame,
+ SequenceGroup seqsel, ColumnSelection colsel,
+ HiddenColumns hidden, SelectionSource source, Object alignFrame)
+ {
+ // System.err.println("Testing selection event relay to
+ // jsfunction:"+_listener);
+ String setid = "";
+ AlignFrame src = (AlignFrame) alignFrame;
+ if (source != null)
+ {
+ if (source instanceof AlignViewport
+ && ((AlignFrame) currentFrame).getViewport() == source)
+ {
+ // should be valid if it just generated an event!
+ src = (AlignFrame) currentFrame;
+
+ }
+ }
+ String[] seqs = new String[] {};
+ String[] cols = new String[] {};
+ int strt = 0, end = (src == null) ? -1
+ : src.alignPanel.av.getAlignment().getWidth();
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ seqs = new String[seqsel.getSize()];
+ for (int i = 0; i < seqs.length; i++)
+ {
+ seqs[i] = seqsel.getSequenceAt(i).getName();
+ }
+ if (strt < seqsel.getStartRes())
+ {
+ strt = seqsel.getStartRes();
+ }
+ if (end == -1 || end > seqsel.getEndRes())
+ {
+ end = seqsel.getEndRes();
+ }
+ }
+ if (colsel != null && !colsel.isEmpty())
+ {
+ if (end == -1)
+ {
+ end = colsel.getMax() + 1;
+ }
+ cols = new String[colsel.getSelected().size()];
+ for (int i = 0; i < cols.length; i++)
+ {
+ cols[i] = "" + (1 + colsel.getSelected().get(i).intValue());
+ }
+ }
+ else
+ {
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ // send a valid range, otherwise we send the empty selection
+ cols = new String[2];
+ cols[0] = "" + (1 + strt) + "-" + (1 + end);
+ }
+ }
+ return new Object[] { src, setid, arrayToSeparatorList(seqs),
+ arrayToSeparatorList(cols) };
+ }
+
+}
\ No newline at end of file
--- /dev/null
+package jalview.bin;
+
+import jalview.gui.AlignFrame;
+import jalview.javascript.JalviewLiteJsApi;
+
+/**
+ * JAL-3369 JalviewJS API BH 2019.07.17
+ *
+ * @author hansonr
+ *
+ */
+public interface JalviewJSApi extends JalviewLiteJsApi
+{
+
+ void showOverview();
+
+ /**
+ * process commandline arguments after the JavaScript application has started
+ *
+ * @param args
+ * @return
+ */
+ Object parseArguments(String[] args);
+
+
+ /**
+ * Open a new Tree panel on the desktop statically. Params are standard (not
+ * set by Groovy). No dialog is opened.
+ *
+ * @param af
+ * may be null
+ * @param treeType
+ * @param modelName
+ * @return null, or the string "label.you_need_at_least_n_sequences" if number
+ * of sequences selected is inappropriate
+ */
+ public Object openTreePanel(AlignFrame af, String treeType,
+ String modelName);
+
+ /**
+ * public static method for JalviewJS API to open a PCAPanel without
+ * necessarily using a dialog.
+ *
+ * @param af
+ * may be null
+ * @param modelName
+ * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
+ * if number of sequences selected is inappropriate
+ */
+ public Object openPcaPanel(AlignFrame af, String modelName);
+
+}
package jalview.bin;
import jalview.analysis.AlignmentUtils;
+import jalview.api.AlignFrameI;
+import jalview.api.AlignViewportI;
+import jalview.api.JalviewApp;
import jalview.api.StructureSelectionManagerProvider;
import jalview.appletgui.AlignFrame;
import jalview.appletgui.AlignViewport;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
import jalview.io.FileFormats;
import jalview.io.FileParse;
import jalview.io.IdentifyFile;
-import jalview.io.JPredFile;
-import jalview.io.JnetAnnotationMaker;
import jalview.io.NewickFile;
import jalview.javascript.JSFunctionExec;
import jalview.javascript.JalviewLiteJsApi;
import jalview.javascript.JsCallBack;
import jalview.javascript.MouseOverStructureListener;
+import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
import jalview.util.ColorUtils;
-import jalview.util.HttpUtils;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.applet.Applet;
import java.awt.Button;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
-import java.util.StringTokenizer;
import java.util.Vector;
import netscape.javascript.JSObject;
* @author $author$
* @version $Revision: 1.92 $
*/
+@SuppressWarnings("serial")
public class JalviewLite extends Applet
- implements StructureSelectionManagerProvider, JalviewLiteJsApi
+ implements StructureSelectionManagerProvider, JalviewLiteJsApi,
+ JalviewApp
{
+ public JalviewLite()
+ {
+ appLoader = new JalviewAppLoader(debug);
+ }
private static final String TRUE = "true";
private static final String FALSE = "false";
return StructureSelectionManager.getStructureSelectionManager(this);
}
+ @Override
+ public StructureSelectionManagerProvider getStructureSelectionManagerProvider()
+ {
+ return this;
+ }
+
// /////////////////////////////////////////
// The following public methods may be called
// externally, eg via javascript in HTML page
* .AlignFrame)
*/
@Override
- public String getSelectedSequencesFrom(AlignFrame alf)
+ public String getSelectedSequencesFrom(AlignFrameI alf)
{
return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
}
* .AlignFrame, java.lang.String)
*/
@Override
- public String getSelectedSequencesFrom(AlignFrame alf, String sep)
+ public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
{
StringBuffer result = new StringBuffer("");
if (sep == null || sep.length() == 0)
{
sep = separator; // "+0x00AC;
}
- if (alf.viewport.getSelectionGroup() != null)
+ if (((AlignFrame) alf).viewport.getSelectionGroup() != null)
{
- SequenceI[] seqs = alf.viewport.getSelectionGroup()
- .getSequencesInOrder(alf.viewport.getAlignment());
+ SequenceI[] seqs = ((AlignFrame) alf).viewport.getSelectionGroup()
+ .getSequencesInOrder(
+ ((AlignFrame) alf).viewport.getAlignment());
for (int i = 0; i < seqs.length; i++)
{
* java.lang.String, java.lang.String, java.lang.String)
*/
@Override
- public void highlightIn(final AlignFrame alf, final String sequenceId,
+ public void highlightIn(final AlignFrameI alf, final String sequenceId,
final String position, final String alignedPosition)
{
// TODO: could try to highlight in all alignments if alf==null
jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
- alf.viewport.getAlignment().getSequencesArray());
+ ((AlignFrame) alf).viewport.getAlignment().getSequencesArray());
final SequenceI sq = matcher.findIdMatch(sequenceId);
if (sq != null)
{
int apos = -1;
try
{
- apos = Integer.valueOf(position).intValue();
+ apos = new Integer(position).intValue();
apos--;
} catch (NumberFormatException ex)
{
* java.lang.String, java.lang.String)
*/
@Override
- public void selectIn(AlignFrame alf, String sequenceIds, String columns)
+ public void selectIn(AlignFrameI alf, String sequenceIds, String columns)
{
selectIn(alf, sequenceIds, columns, separator);
}
* java.lang.String, java.lang.String, java.lang.String)
*/
@Override
- public void selectIn(final AlignFrame alf, String sequenceIds,
+ public void selectIn(final AlignFrameI alf, String sequenceIds,
String columns, String sep)
{
if (sep == null || sep.length() == 0)
}
}
// deparse fields
- String[] ids = separatorListToArray(sequenceIds, sep);
- String[] cols = separatorListToArray(columns, sep);
+ String[] ids = JalviewAppLoader.separatorListToArray(sequenceIds, sep);
+ String[] cols = JalviewAppLoader.separatorListToArray(columns, sep);
final SequenceGroup sel = new SequenceGroup();
final ColumnSelection csel = new ColumnSelection();
- AlignmentI al = alf.viewport.getAlignment();
+ AlignmentI al = ((AlignFrame) alf).viewport.getAlignment();
jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
- alf.viewport.getAlignment().getSequencesArray());
+ ((AlignFrame) alf).viewport.getAlignment().getSequencesArray());
int start = 0, end = al.getWidth(), alw = al.getWidth();
boolean seqsfound = true;
if (ids != null && ids.length > 0)
int from = -1, to = -1;
try
{
- from = Integer.valueOf(cl.substring(0, p)).intValue();
+ from = new Integer(cl.substring(0, p)).intValue();
from--;
} catch (NumberFormatException ex)
{
}
try
{
- to = Integer.valueOf(cl.substring(p + 1)).intValue();
+ to = new Integer(cl.substring(p + 1)).intValue();
to--;
} catch (NumberFormatException ex)
{
int r = -1;
try
{
- r = Integer.valueOf(cl).intValue();
+ r = new Integer(cl).intValue();
r--;
} catch (NumberFormatException ex)
{
@Override
public void run()
{
- alf.select(sel, csel,
- alf.getAlignViewport().getAlignment().getHiddenColumns());
+ ((AlignFrame) alf).select(sel, csel, ((AlignFrame) alf)
+ .getAlignViewport().getAlignment().getHiddenColumns());
}
});
}
* .appletgui.AlignFrame, java.lang.String, java.lang.String)
*/
@Override
- public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
String format, String suffix)
{
try
{
FileFormatI theFormat = FileFormats.getInstance().forName(format);
boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
- if (alf.viewport.getSelectionGroup() != null)
+ if (((AlignFrame) alf).viewport.getSelectionGroup() != null)
{
// JBPNote: getSelectionAsNewSequence behaviour has changed - this
// method now returns a full copy of sequence data
// TODO consider using getSequenceSelection instead here
String reply = new AppletFormatAdapter().formatSequences(theFormat,
- new Alignment(alf.viewport.getSelectionAsNewSequence()),
+ new Alignment(((AlignFrame) alf).viewport
+ .getSelectionAsNewSequence()),
seqlimits);
return reply;
}
* )
*/
@Override
- public String getAlignmentOrderFrom(AlignFrame alf)
+ public String getAlignmentOrderFrom(AlignFrameI alf)
{
return getAlignmentOrderFrom(alf, separator);
}
* , java.lang.String)
*/
@Override
- public String getAlignmentOrderFrom(AlignFrame alf, String sep)
+ public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
{
- AlignmentI alorder = alf.getAlignViewport().getAlignment();
+ AlignmentI alorder = ((AlignFrame) alf).getAlignViewport()
+ .getAlignment();
String[] order = new String[alorder.getHeight()];
for (int i = 0; i < order.length; i++)
{
* java.lang.String, java.lang.String, java.lang.String)
*/
@Override
- public String orderAlignmentBy(AlignFrame alf, String order,
+ public String orderAlignmentBy(AlignFrameI alf, String order,
String undoName, String sep)
{
- String[] ids = separatorListToArray(order, sep);
+ String[] ids = JalviewAppLoader.separatorListToArray(order, sep);
SequenceI[] sqs = null;
if (ids != null && ids.length > 0)
{
jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
- alf.viewport.getAlignment().getSequencesArray());
+ ((AlignFrame) alf).viewport.getAlignment()
+ .getSequencesArray());
int s = 0;
sqs = new SequenceI[ids.length];
for (int i = 0; i < ids.length; i++)
final String _undoName = undoName;
// TODO: deal with synchronization here: cannot raise any events until after
// this has returned.
- return alf.sortBy(aorder, _undoName) ? TRUE : "";
+ return ((AlignFrame) alf).sortBy(aorder, _undoName) ? TRUE : "";
}
/*
* java.lang.String)
*/
@Override
- public String getAlignmentFrom(AlignFrame alf, String format)
+ public String getAlignmentFrom(AlignFrameI alf, String format)
{
return getAlignmentFrom(alf, format, TRUE);
}
* java.lang.String, java.lang.String)
*/
@Override
- public String getAlignmentFrom(AlignFrame alf, String format,
+ public String getAlignmentFrom(AlignFrameI alf, String format,
String suffix)
{
try
FileFormatI theFormat = FileFormats.getInstance().forName(format);
String reply = new AppletFormatAdapter().formatSequences(theFormat,
- alf.viewport.getAlignment(), seqlimits);
+ ((AlignFrame) alf).viewport.getAlignment(), seqlimits);
return reply;
} catch (IllegalArgumentException ex)
{
* , java.lang.String)
*/
@Override
- public void loadAnnotationFrom(AlignFrame alf, String annotation)
+ public void loadAnnotationFrom(AlignFrameI alf, String annotation)
{
- if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(),
+ if (new AnnotationFile().annotateAlignmentView(
+ ((AlignFrame) alf).getAlignViewport(),
annotation, DataSourceType.PASTE))
{
- alf.alignPanel.fontChanged();
- alf.alignPanel.setScrollValues(0, 0);
+ ((AlignFrame) alf).alignPanel.fontChanged();
+ ((AlignFrame) alf).alignPanel.setScrollValues(0, 0);
}
else
{
- alf.parseFeaturesFile(annotation, DataSourceType.PASTE);
+ ((AlignFrame) alf).parseFeaturesFile(annotation,
+ DataSourceType.PASTE);
}
}
* , java.lang.String)
*/
@Override
- public boolean loadFeaturesFrom(AlignFrame alf, String features,
+ public boolean loadFeaturesFrom(AlignFrameI alf, String features,
boolean autoenabledisplay)
{
- return alf.parseFeaturesFile(features, DataSourceType.PASTE,
+ return ((AlignFrame) alf).parseFeaturesFile(features,
+ DataSourceType.PASTE,
autoenabledisplay);
}
* java.lang.String)
*/
@Override
- public String getFeaturesFrom(AlignFrame alf, String format)
+ public String getFeaturesFrom(AlignFrameI alf, String format)
{
- return alf.outputFeatures(false, format);
+ return ((AlignFrame) alf).outputFeatures(false, format);
}
/*
* )
*/
@Override
- public String getAnnotationFrom(AlignFrame alf)
+ public String getAnnotationFrom(AlignFrameI alf)
{
- return alf.outputAnnotations(false);
+ return ((AlignFrame) alf).outputAnnotations(false);
}
/*
* @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
*/
@Override
- public AlignFrame newViewFrom(AlignFrame alf)
+ public AlignFrame newViewFrom(AlignFrameI alf)
{
- return alf.newView(null);
+ return ((AlignFrame) alf).newView(null);
}
/*
* java.lang.String)
*/
@Override
- public AlignFrame newViewFrom(AlignFrame alf, String name)
+ public AlignFrame newViewFrom(AlignFrameI alf, String name)
{
- return alf.newView(name);
+ return ((AlignFrame) alf).newView(name);
}
/*
* , java.lang.String)
*/
@Override
- public void setMouseoverListener(AlignFrame af, String listener)
+ public void setMouseoverListener(AlignFrameI af, String listener)
{
if (listener != null)
{
}
}
jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
- this, af, listener);
+ this, (AlignFrame) af, listener, debug);
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
.addStructureViewerListener(mol);
System.err.println("Added a mouseover listener for "
+ ((af == null) ? "All frames"
: "Just views for "
- + af.getAlignViewport().getSequenceSetId()));
+ + ((AlignFrame) af).getAlignViewport()
+ .getSequenceSetId()));
System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
* , java.lang.String)
*/
@Override
- public void setSelectionListener(AlignFrame af, String listener)
+ public void setSelectionListener(AlignFrameI af, String listener)
{
if (listener != null)
{
}
}
jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
- this, af, listener);
+ this, (AlignFrame) af, listener, debug);
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
.addSelectionListener(mol);
System.err.println("Added a selection listener for "
+ ((af == null) ? "All frames"
: "Just views for "
- + af.getAlignViewport().getSequenceSetId()));
+ + ((AlignFrame) af).getAlignViewport()
+ .getSequenceSetId()));
System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
}
}
MouseOverStructureListener mol = new MouseOverStructureListener(this,
- listener, separatorListToArray(modelSet));
+ listener, separatorListToArray(modelSet), debug);
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
.addStructureViewerListener(mol);
* .AlignFrame, java.lang.String)
*/
@Override
- public void removeJavascriptListener(AlignFrame af, String listener)
+ public void removeJavascriptListener(AlignFrameI af, String listener)
{
if (listener != null)
{
}
if (jsFunctionExec != null)
{
- jsFunctionExec.stopQueue();
- jsFunctionExec.jvlite = null;
+ jsFunctionExec.tidyUp();
+ jsFunctionExec = null;
}
initialAlignFrame = null;
- jsFunctionExec = null;
javascriptListeners = null;
StructureSelectionManager.release(this);
}
try
{
StructureSelectionManager.getStructureSelectionManager(me)
- .mouseOverStructure(Integer.valueOf(pdbResNum).intValue(),
+ .mouseOverStructure(new Integer(pdbResNum).intValue(),
chain, pdbfile);
if (debug)
{
* java.lang.String, java.lang.String)
*/
@Override
- public void scrollViewToIn(final AlignFrame alf, final String topRow,
+ public void scrollViewToIn(final AlignFrameI alf, final String topRow,
final String leftHandColumn)
{
java.awt.EventQueue.invokeLater(new Runnable()
{
try
{
- alf.scrollTo(Integer.valueOf(topRow).intValue(),
- Integer.valueOf(leftHandColumn).intValue());
+ ((AlignFrame) alf).scrollTo(new Integer(topRow).intValue(),
+ new Integer(leftHandColumn).intValue());
} catch (Exception ex)
{
* .AlignFrame, java.lang.String)
*/
@Override
- public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
+ public void scrollViewToRowIn(final AlignFrameI alf, final String topRow)
{
java.awt.EventQueue.invokeLater(new Runnable()
{
try
{
- alf.scrollToRow(Integer.valueOf(topRow).intValue());
+ ((AlignFrame) alf).scrollToRow(new Integer(topRow).intValue());
} catch (Exception ex)
{
* .AlignFrame, java.lang.String)
*/
@Override
- public void scrollViewToColumnIn(final AlignFrame alf,
+ public void scrollViewToColumnIn(final AlignFrameI alf,
final String leftHandColumn)
{
java.awt.EventQueue.invokeLater(new Runnable()
{
try
{
- alf.scrollToColumn(Integer.valueOf(leftHandColumn).intValue());
+ ((AlignFrame) alf)
+ .scrollToColumn(new Integer(leftHandColumn).intValue());
} catch (Exception ex)
{
boolean embedded = false;
- private boolean checkForJmol = true;
+ boolean checkForJmol = true;
- private boolean checkedForJmol = false; // ensure we don't check for jmol
+ boolean checkedForJmol = false; // ensure we don't check for jmol
// every time the app is re-inited
*/
public boolean useXtrnalSviewer = false;
+ public JalviewAppLoader appLoader;
+
+ public AlignFrame loaderFrame;
+
public static boolean debug = false;
static String builddate = null, version = null, installation = null;
.getString("error.invalid_separator_parameter"));
}
}
+
+ // Background color
+
int r = 255;
int g = 255;
int b = 255;
b = 255;
}
}
+ setBackground(new Color(r, g, b));
+
param = getParameter("label");
if (param != null)
{
launcher.setLabel(param);
}
- setBackground(new Color(r, g, b));
-
file = getParameter("file");
if (file == null)
{
- // Maybe the sequences are added as parameters
- StringBuffer data = new StringBuffer("PASTE");
- int i = 1;
- while ((file = getParameter("sequence" + i)) != null)
- {
- data.append(file.toString() + "\n");
- i++;
- }
- if (data.length() > 5)
- {
- file = data.toString();
- }
+ file = appLoader.getPastedSequence(this);
}
if (getDefaultParameter("enableSplitFrame", true))
{
file2 = getParameter("file2");
}
- embedded = TRUE.equalsIgnoreCase(getParameter("embedded"));
+ embedded = (TRUE.equalsIgnoreCase(getParameter("embedded"))
+ || file != null
+ && FALSE.equalsIgnoreCase(getParameter("showbutton")));
if (embedded)
{
- LoadingThread loader = new LoadingThread(file, file2, this);
- loader.start();
- }
- else if (file != null)
- {
- /*
- * Start the applet immediately or show a button to start it
- */
- if (FALSE.equalsIgnoreCase(getParameter("showbutton")))
- {
- LoadingThread loader = new LoadingThread(file, file2, this);
- loader.start();
- }
- else
- {
- add(launcher);
- launcher.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- LoadingThread loader = new LoadingThread(file, file2,
- JalviewLite.this);
- loader.start();
- }
- });
- }
+ startLoading();
}
- else
+ else if (file == null)
{
// jalview initialisation with no alignment. loadAlignment() method can
// still be called to open new alignments.
fileFound = false;
callInitCallback();
}
+ else
+ {
+ add(launcher);
+ launcher.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ startLoading();
+ }
+ });
+ }
+ }
+
+ protected void startLoading()
+ {
+ LoadingThread loader = new LoadingThread(file, file2, this);
+ loader.start();
}
private void initLiveConnect()
}
}
- private void callInitCallback()
+ void callInitCallback()
{
String initjscallback = getParameter("oninit");
if (initjscallback == null)
try
{
// do onInit with the JS executor thread
- new JSFunctionExec(this).executeJavascriptFunction(true,
+ new JSFunctionExec(this, debug).executeJavascriptFunction(true,
initjscallback, null,
"Calling oninit callback '" + initjscallback + "'.");
} catch (Exception e)
JalviewLite applet;
- private void dbgMsg(String msg)
+ public void dbgMsg(String msg)
{
if (JalviewLite.debug)
{
*/
public String resolveFileProtocol(String path)
{
- /*
- * is it paste data?
- */
- if (path.startsWith("PASTE"))
- {
- protocol = DataSourceType.PASTE;
- return path.substring(5);
- }
- /*
- * is it a URL?
- */
- if (path.indexOf("://") != -1)
- {
- protocol = DataSourceType.URL;
- return path;
- }
-
- /*
- * try relative to document root
- */
- URL documentBase = getDocumentBase();
- String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase);
- if (HttpUtils.isValidUrl(withDocBase))
- {
- if (debug)
- {
- System.err.println("Prepended document base '" + documentBase
- + "' to make: '" + withDocBase + "'");
- }
- protocol = DataSourceType.URL;
- return withDocBase;
- }
-
- /*
- * try relative to codebase (if different to document base)
- */
- URL codeBase = getCodeBase();
- String withCodeBase = applet.resolveUrlForLocalOrAbsolute(path,
- codeBase);
- if (!withCodeBase.equals(withDocBase)
- && HttpUtils.isValidUrl(withCodeBase))
- {
- protocol = DataSourceType.URL;
- if (debug)
- {
- System.err.println("Prepended codebase '" + codeBase
- + "' to make: '" + withCodeBase + "'");
- }
- return withCodeBase;
- }
-
- /*
- * try locating by classloader; try this last so files in the directory
- * are resolved using document base
- */
- if (inArchive(path))
- {
- protocol = DataSourceType.CLASSLOADER;
- }
- return path;
+ String[] ret = new String[] { path };
+ protocol = JalviewAppLoader.resolveFileProtocol(applet, ret);
+ return ret[0];
}
public LoadingThread(String file, String file2, JalviewLite _applet)
if (newAlignFrame != null)
{
addToDisplay(newAlignFrame, newAlignFrame2);
- loadTree(newAlignFrame);
-
- loadScoreFile(newAlignFrame);
-
- loadFeatures(newAlignFrame);
-
- loadAnnotations(newAlignFrame);
-
- loadJnetFile(newAlignFrame);
-
- loadPdbFiles(newAlignFrame);
+ applet.loaderFrame = newAlignFrame;
+ appLoader.load(applet);
}
else
{
fileFound = false;
applet.remove(launcher);
applet.repaint();
+ callInitCallback();
}
- callInitCallback();
}
/**
return null;
}
- /**
- * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
- * else false.
- *
- * @param alignFrame
- * @return
- */
- protected boolean loadPdbFiles(AlignFrame alignFrame)
- {
- boolean result = false;
- /*
- * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 -
- * related to JAL-434
- */
-
- applet.setAlignPdbStructures(
- getDefaultParameter("alignpdbfiles", false));
- /*
- * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
- * PDB|1GAQ|1GAQ|C">
- *
- * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
- *
- * <param name="PDBfile3" value="1q0o Q45135_9MICO">
- */
-
- int pdbFileCount = 0;
- // Accumulate pdbs here if they are heading for the same view (if
- // alignPdbStructures is true)
- Vector pdbs = new Vector();
- // create a lazy matcher if we're asked to
- jalview.analysis.SequenceIdMatcher matcher = (applet
- .getDefaultParameter("relaxedidmatch", false))
- ? new jalview.analysis.SequenceIdMatcher(
- alignFrame.getAlignViewport().getAlignment()
- .getSequencesArray())
- : null;
-
- String param;
- do
- {
- if (pdbFileCount > 0)
- {
- param = applet.getParameter("PDBFILE" + pdbFileCount);
- }
- else
- {
- param = applet.getParameter("PDBFILE");
- }
-
- if (param != null)
- {
- PDBEntry pdb = new PDBEntry();
-
- String seqstring;
- SequenceI[] seqs = null;
- String[] chains = null;
-
- StringTokenizer st = new StringTokenizer(param, " ");
-
- if (st.countTokens() < 2)
- {
- String sequence = applet.getParameter("PDBSEQ");
- if (sequence != null)
- {
- seqs = new SequenceI[] { matcher == null
- ? (Sequence) alignFrame.getAlignViewport()
- .getAlignment().findName(sequence)
- : matcher.findIdMatch(sequence) };
- }
-
- }
- else
- {
- param = st.nextToken();
- List<SequenceI> tmp = new ArrayList<>();
- List<String> tmp2 = new ArrayList<>();
-
- while (st.hasMoreTokens())
- {
- seqstring = st.nextToken();
- StringTokenizer st2 = new StringTokenizer(seqstring, "=");
- if (st2.countTokens() > 1)
- {
- // This is the chain
- tmp2.add(st2.nextToken());
- seqstring = st2.nextToken();
- }
- tmp.add(matcher == null
- ? (Sequence) alignFrame.getAlignViewport()
- .getAlignment().findName(seqstring)
- : matcher.findIdMatch(seqstring));
- }
-
- seqs = tmp.toArray(new SequenceI[tmp.size()]);
- if (tmp2.size() == tmp.size())
- {
- chains = tmp2.toArray(new String[tmp2.size()]);
- }
- }
- param = resolveFileProtocol(param);
- // TODO check JAL-357 for files in a jar (CLASSLOADER)
- pdb.setFile(param);
-
- if (seqs != null)
- {
- for (int i = 0; i < seqs.length; i++)
- {
- if (seqs[i] != null)
- {
- ((Sequence) seqs[i]).addPDBId(pdb);
- StructureSelectionManager
- .getStructureSelectionManager(applet)
- .registerPDBEntry(pdb);
- }
- else
- {
- if (JalviewLite.debug)
- {
- // this may not really be a problem but we give a warning
- // anyway
- System.err.println(
- "Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
- + i + ")");
- }
- }
- }
-
- if (!alignPdbStructures)
- {
- alignFrame.newStructureView(applet, pdb, seqs, chains,
- protocol);
- }
- else
- {
- pdbs.addElement(new Object[] { pdb, seqs, chains, protocol });
- }
- }
- }
-
- pdbFileCount++;
- } while (param != null || pdbFileCount < 10);
- if (pdbs.size() > 0)
- {
- SequenceI[][] seqs = new SequenceI[pdbs.size()][];
- PDBEntry[] pdb = new PDBEntry[pdbs.size()];
- String[][] chains = new String[pdbs.size()][];
- String[] protocols = new String[pdbs.size()];
- for (int pdbsi = 0, pdbsiSize = pdbs
- .size(); pdbsi < pdbsiSize; pdbsi++)
- {
- Object[] o = (Object[]) pdbs.elementAt(pdbsi);
- pdb[pdbsi] = (PDBEntry) o[0];
- seqs[pdbsi] = (SequenceI[]) o[1];
- chains[pdbsi] = (String[]) o[2];
- protocols[pdbsi] = (String) o[3];
- }
- alignFrame.alignedStructureView(applet, pdb, seqs, chains,
- protocols);
- result = true;
- }
- return result;
- }
-
- /**
- * Load in a Jnetfile if specified by parameter. Returns true if loaded,
- * else false.
- *
- * @param alignFrame
- * @return
- */
- protected boolean loadJnetFile(AlignFrame alignFrame)
- {
- boolean result = false;
- String param = applet.getParameter("jnetfile");
- if (param == null)
- {
- // jnet became jpred around 2016
- param = applet.getParameter("jpredfile");
- }
- if (param != null)
- {
- try
- {
- param = resolveFileProtocol(param);
- JPredFile predictions = new JPredFile(param, protocol);
- JnetAnnotationMaker.add_annotation(predictions,
- alignFrame.viewport.getAlignment(), 0, false);
- // false == do not add sequence profile from concise output
-
- alignFrame.viewport.getAlignment().setupJPredAlignment();
-
- alignFrame.alignPanel.fontChanged();
- alignFrame.alignPanel.setScrollValues(0, 0);
- result = true;
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- return result;
- }
-
- /**
- * Load annotations if specified by parameter. Returns true if loaded, else
- * false.
- *
- * @param alignFrame
- * @return
- */
- protected boolean loadAnnotations(AlignFrame alignFrame)
- {
- boolean result = false;
- String param = applet.getParameter("annotations");
- if (param != null)
- {
- param = resolveFileProtocol(param);
-
- if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
- param, protocol))
- {
- alignFrame.alignPanel.fontChanged();
- alignFrame.alignPanel.setScrollValues(0, 0);
- result = true;
- }
- else
- {
- System.err.println(
- "Annotations were not added from annotation file '"
- + param + "'");
- }
- }
- return result;
- }
-
- /**
- * Load features file and view settings as specified by parameters. Returns
- * true if features were loaded, else false.
- *
- * @param alignFrame
- * @return
- */
- protected boolean loadFeatures(AlignFrame alignFrame)
- {
- boolean result = false;
- // ///////////////////////////
- // modify display of features
- // we do this before any features have been loaded, ensuring any hidden
- // groups are hidden when features first displayed
- //
- // hide specific groups
- //
- String param = applet.getParameter("hidefeaturegroups");
- if (param != null)
- {
- alignFrame.setFeatureGroupState(separatorListToArray(param), false);
- // applet.setFeatureGroupStateOn(newAlignFrame, param, false);
- }
- // show specific groups
- param = applet.getParameter("showfeaturegroups");
- if (param != null)
- {
- alignFrame.setFeatureGroupState(separatorListToArray(param), true);
- // applet.setFeatureGroupStateOn(newAlignFrame, param, true);
- }
- // and now load features
- param = applet.getParameter("features");
- if (param != null)
- {
- param = resolveFileProtocol(param);
-
- result = alignFrame.parseFeaturesFile(param, protocol);
- }
-
- param = applet.getParameter("showFeatureSettings");
- if (param != null && param.equalsIgnoreCase(TRUE))
- {
- alignFrame.viewport.setShowSequenceFeatures(true);
- new FeatureSettings(alignFrame.alignPanel);
- }
- return result;
- }
-
- /**
- * Load a score file if specified by parameter. Returns true if file was
- * loaded, else false.
- *
- * @param alignFrame
- */
- protected boolean loadScoreFile(AlignFrame alignFrame)
- {
- boolean result = false;
- String sScoreFile = applet.getParameter("scoreFile");
- if (sScoreFile != null && !"".equals(sScoreFile))
- {
- try
- {
- if (debug)
- {
- System.err.println(
- "Attempting to load T-COFFEE score file from the scoreFile parameter");
- }
- result = alignFrame.loadScoreFile(sScoreFile);
- if (!result)
- {
- System.err.println(
- "Failed to parse T-COFFEE parameter as a valid score file ('"
- + sScoreFile + "')");
- }
- } catch (Exception e)
- {
- System.err.printf("Cannot read score file: '%s'. Cause: %s \n",
- sScoreFile, e.getMessage());
- }
- }
- return result;
- }
-
- /**
- * Load a tree for the alignment if specified by parameter. Returns true if
- * a tree was loaded, else false.
- *
- * @param alignFrame
- * @return
- */
- protected boolean loadTree(AlignFrame alignFrame)
- {
- boolean result = false;
- String treeFile = applet.getParameter("tree");
- if (treeFile == null)
- {
- treeFile = applet.getParameter("treeFile");
- }
-
- if (treeFile != null)
- {
- try
- {
- treeFile = resolveFileProtocol(treeFile);
- NewickFile fin = new NewickFile(treeFile, protocol);
- fin.parse();
-
- if (fin.getTree() != null)
- {
- alignFrame.loadTree(fin, treeFile);
- result = true;
- dbgMsg("Successfully imported tree.");
- }
- else
- {
- dbgMsg("Tree parameter did not resolve to a valid tree.");
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- return result;
- }
-
- /**
- * Discovers whether the given file is in the Applet Archive
- *
- * @param f
- * String
- * @return boolean
- */
- boolean inArchive(String f)
- {
- // This might throw a security exception in certain browsers
- // Netscape Communicator for instance.
- try
- {
- boolean rtn = (getClass().getResourceAsStream("/" + f) != null);
- if (debug)
- {
- System.err.println("Resource '" + f + "' was "
- + (rtn ? "" : "not ") + "located by classloader.");
- }
- return rtn;
- } catch (Exception ex)
- {
- System.out.println("Exception checking resources: " + f + " " + ex);
- return false;
- }
- }
}
/**
/**
* set to enable the URL based javascript execution mechanism
*/
- public boolean jsfallbackEnabled = false;
+ private boolean jsfallbackEnabled = false;
/**
* parse the string into a list
* @param list
* @return elements separated by separator
*/
+ @Override
public String[] separatorListToArray(String list)
{
- return separatorListToArray(list, separator);
- }
-
- /**
- * parse the string into a list
- *
- * @param list
- * @param separator
- * @return elements separated by separator
- */
- public static String[] separatorListToArray(String list, String separator)
- {
- // TODO use StringUtils version (slightly different...)
- int seplen = separator.length();
- if (list == null || list.equals("") || list.equals(separator))
- {
- return null;
- }
- java.util.Vector jv = new Vector();
- int cp = 0, pos;
- while ((pos = list.indexOf(separator, cp)) > cp)
- {
- jv.addElement(list.substring(cp, pos));
- cp = pos + seplen;
- }
- if (cp < list.length())
- {
- String c = list.substring(cp);
- if (!c.equals(separator))
- {
- jv.addElement(c);
- }
- }
- if (jv.size() > 0)
- {
- String[] v = new String[jv.size()];
- for (int i = 0; i < v.length; i++)
- {
- v[i] = (String) jv.elementAt(i);
- }
- jv.removeAllElements();
- if (debug)
- {
- System.err.println("Array from '" + separator
- + "' separated List:\n" + v.length);
- for (int i = 0; i < v.length; i++)
- {
- System.err.println("item " + i + " '" + v[i] + "'");
- }
- }
- return v;
- }
- if (debug)
- {
- System.err.println(
- "Empty Array from '" + separator + "' separated List");
- }
- return null;
+ return JalviewAppLoader.separatorListToArray(list, separator);
}
/**
* @param list
* @return concatenated string
*/
+ @Override
public String arrayToSeparatorList(String[] list)
{
- return arrayToSeparatorList(list, separator);
- }
-
- /**
- * concatenate the list with separator
- *
- * @param list
- * @param separator
- * @return concatenated string
- */
- public static String arrayToSeparatorList(String[] list, String separator)
- {
- // TODO use StringUtils version
- StringBuffer v = new StringBuffer();
- if (list != null && list.length > 0)
- {
- for (int i = 0, iSize = list.length; i < iSize; i++)
- {
- if (list[i] != null)
- {
- if (i > 0)
- {
- v.append(separator);
- }
- v.append(list[i]);
- }
- }
- if (debug)
- {
- System.err
- .println("Returning '" + separator + "' separated List:\n");
- System.err.println(v);
- }
- return v.toString();
- }
- if (debug)
- {
- System.err.println(
- "Returning empty '" + separator + "' separated List\n");
- }
- return "" + separator;
+ return JalviewAppLoader.arrayToSeparatorList(list, separator);
}
/*
* )
*/
@Override
- public String getFeatureGroupsOn(AlignFrame alf)
+ public String getFeatureGroupsOn(AlignFrameI alf)
{
- String lst = arrayToSeparatorList(alf.getFeatureGroups());
+ String lst = arrayToSeparatorList(
+ ((AlignFrame) alf).getFeatureGroups());
return lst;
}
* .AlignFrame, boolean)
*/
@Override
- public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
+ public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
{
- return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
+ return arrayToSeparatorList(
+ ((AlignFrame) alf).getFeatureGroupsOfState(visible));
}
/*
* AlignFrame, java.lang.String, boolean)
*/
@Override
- public void setFeatureGroupStateOn(final AlignFrame alf,
+ public void setFeatureGroupStateOn(final AlignFrameI alf,
final String groups, boolean state)
{
final boolean st = state;// !(state==null || state.equals("") ||
@Override
public void run()
{
- alf.setFeatureGroupState(separatorListToArray(groups), st);
+ ((AlignFrame) alf)
+ .setFeatureGroupState(separatorListToArray(groups), st);
}
});
}
* the value to return otherwise
* @return true or false
*/
+ @Override
public boolean getDefaultParameter(String name, boolean def)
{
String stn;
* java.lang.String, java.lang.String, java.lang.String)
*/
@Override
- public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
+ public boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
String pdbEntryString, String pdbFile)
{
- return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
+ return ((AlignFrame) alFrame).addPdbFile(sequenceId, pdbEntryString,
+ pdbFile);
}
- protected void setAlignPdbStructures(boolean alignPdbStructures)
+ @Override
+ public void setAlignPdbStructures(boolean alignPdbStructures)
{
this.alignPdbStructures = alignPdbStructures;
}
// callInitCallback();
}
- private Hashtable<String, long[]> jshashes = new Hashtable<>();
+ private Hashtable<String, int[]> jshashes = new Hashtable<>();
private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<>();
- public void setJsMessageSet(String messageclass, String viewId,
- String[] colcommands)
- {
- Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
- if (msgset == null)
- {
- msgset = new Hashtable<>();
- jsmessages.put(messageclass, msgset);
- }
- msgset.put(viewId, colcommands);
- long[] l = new long[colcommands.length];
- for (int i = 0; i < colcommands.length; i++)
- {
- l[i] = colcommands[i].hashCode();
- }
- jshashes.put(messageclass + "|" + viewId, l);
- }
- /*
- * (non-Javadoc)
- *
- * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
- * java.lang.String)
- */
@Override
- public String getJsMessage(String messageclass, String viewId)
+ public Hashtable<String, int[]> getJSHashes()
{
- Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
- if (msgset != null)
- {
- String[] msgs = msgset.get(viewId);
- if (msgs != null)
- {
- for (int i = 0; i < msgs.length; i++)
- {
- if (msgs[i] != null)
- {
- String m = msgs[i];
- msgs[i] = null;
- return m;
- }
- }
- }
- }
- return "";
+ return jshashes;
}
- public boolean isJsMessageSetChanged(String string, String string2,
- String[] colcommands)
+ @Override
+ public Hashtable<String, Hashtable<String, String[]>> getJSMessages()
{
- long[] l = jshashes.get(string + "|" + string2);
- if (l == null && colcommands != null)
- {
- return true;
- }
- for (int i = 0; i < colcommands.length; i++)
- {
- if (l[i] != colcommands[i].hashCode())
- {
- return true;
- }
- }
- return false;
+ return jsmessages;
}
- private Vector jsExecQueue = new Vector();
+ private Vector<Runnable> jsExecQueue = new Vector<>();
- public Vector getJsExecQueue()
+ @Override
+ public Vector<Runnable> getJsExecQueue(JSFunctionExec exec)
{
+ jsFunctionExec = exec;
return jsExecQueue;
}
- public void setExecutor(JSFunctionExec jsFunctionExec2)
- {
- jsFunctionExec = jsFunctionExec2;
- }
+ // public void setExecutor(JSFunctionExec jsFunctionExec2)
+ // {
+ // jsFunctionExec = jsFunctionExec2;
+ // }
/**
* return the given colour value parameter or the given default if parameter
}
/**
- * form a complete URL given a path to a resource and a reference location on
- * the same server
- *
- * @param targetPath
- * - an absolute path on the same server as localref or a document
- * located relative to localref
- * @param localref
- * - a URL on the same server as url
- * @return a complete URL for the resource located by url
- */
- private String resolveUrlForLocalOrAbsolute(String targetPath,
- URL localref)
- {
- String resolvedPath = "";
- if (targetPath.startsWith("/"))
- {
- String codebase = localref.toString();
- String localfile = localref.getFile();
- resolvedPath = codebase.substring(0,
- codebase.length() - localfile.length()) + targetPath;
- return resolvedPath;
- }
-
- /*
- * get URL path and strip off any trailing file e.g.
- * www.jalview.org/examples/index.html#applets?a=b is trimmed to
- * www.jalview.org/examples/
- */
- String urlPath = localref.toString();
- String directoryPath = urlPath;
- int lastSeparator = directoryPath.lastIndexOf("/");
- if (lastSeparator > 0)
- {
- directoryPath = directoryPath.substring(0, lastSeparator + 1);
- }
-
- if (targetPath.startsWith("/"))
- {
- /*
- * construct absolute URL to a file on the server - this is not allowed?
- */
- // String localfile = localref.getFile();
- // resolvedPath = urlPath.substring(0,
- // urlPath.length() - localfile.length())
- // + targetPath;
- resolvedPath = directoryPath + targetPath.substring(1);
- }
- else
- {
- resolvedPath = directoryPath + targetPath;
- }
- if (debug)
- {
- System.err.println(
- "resolveUrlForLocalOrAbsolute returning " + resolvedPath);
- }
- return resolvedPath;
- }
-
- /**
* open a URL in the browser - resolving it according to relative refs and
* coping with javascript: protocol if necessary.
*
// form valid URL
// Should really use docbase, not codebase.
URL prepend;
- url = resolveUrlForLocalOrAbsolute(url,
+ url = JalviewAppLoader.resolveUrlForLocalOrAbsolute(url,
prepend = getDefaultParameter("resolvetocodebase", false)
? getCodeBase()
: getDocumentBase());
}
}
- /**
- * bind structures in a viewer to any matching sequences in an alignFrame (use
- * sequenceIds to limit scope of search to specific sequences)
- *
- * @param alFrame
- * @param viewer
- * @param sequenceIds
- * @return TODO: consider making an exception structure for indicating when
- * binding fails public SequenceStructureBinding
- * addStructureViewInstance( AlignFrame alFrame, Object viewer, String
- * sequenceIds) {
- *
- * if (sequenceIds != null && sequenceIds.length() > 0) { return
- * alFrame.addStructureViewInstance(viewer,
- * separatorListToArray(sequenceIds)); } else { return
- * alFrame.addStructureViewInstance(viewer, null); } // return null; }
- */
+ @Override
+ public AlignViewportI getViewport()
+ {
+ return loaderFrame.getAlignViewport();
+ }
+
+ @Override
+ public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
+ String[] chains, DataSourceType protocol)
+ {
+ loaderFrame.newStructureView(this, pdb, seqs, chains,
+ protocol);
+ }
+
+ @Override
+ public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
+ String[][] chains, String[] protocols)
+ {
+ loaderFrame.alignedStructureView(this, pdb, seqs, chains, protocols);
+ }
+
+ @Override
+ public void updateForAnnotations()
+ {
+ loaderFrame.alignPanel.fontChanged();
+ loaderFrame.alignPanel.setScrollValues(0, 0);
+ }
+
+ @Override
+ public void setFeatureGroupState(String[] groups, boolean state)
+ {
+ loaderFrame.setFeatureGroupState(groups, state);
+ }
+
+ @Override
+ public boolean parseFeaturesFile(String param, DataSourceType protocol)
+ {
+ return loaderFrame.parseFeaturesFile(param, protocol);
+ }
+
+ @Override
+ public void newFeatureSettings()
+ {
+ getViewport().setShowSequenceFeatures(true);
+ new FeatureSettings(loaderFrame.alignPanel);
+ }
+
+ @Override
+ public boolean loadScoreFile(String sScoreFile) throws IOException
+ {
+ return loaderFrame.loadScoreFile(sScoreFile);
+ }
+
+ @Override
+ public void loadTree(NewickFile tree, String treeFile) throws IOException
+ {
+ loaderFrame.loadTree(tree, treeFile);
+ }
+
+ @Override
+ public boolean isJsfallbackEnabled()
+ {
+ return jsfallbackEnabled;
+ }
+
+ @Override
+ public JSObject getJSObject()
+ {
+ return JSObject.getWindow(this);
+ }
+
+ @Override
+ public void updateColoursFromMouseOver(Object source,
+ MouseOverStructureListener listener)
+ {
+ }
+
+ @Override
+ public Object[] getSelectionForListener(SequenceGroup seqsel, ColumnSelection colsel,
+ HiddenColumns hidden, SelectionSource source, Object alignFrame)
+ {
+ // System.err.println("Testing selection event relay to
+ // jsfunction:"+_listener);
+ String setid = "";
+ AlignFrame src = (AlignFrame) alignFrame;
+ if (source != null)
+ {
+ if (source instanceof jalview.appletgui.AlignViewport
+ && ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame.viewport == source)
+ {
+ // should be valid if it just generated an event!
+ src = ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame;
+
+ }
+ }
+ String[] seqs = new String[] {};
+ String[] cols = new String[] {};
+ int strt = 0, end = (src == null) ? -1
+ : src.alignPanel.av.getAlignment().getWidth();
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ seqs = new String[seqsel.getSize()];
+ for (int i = 0; i < seqs.length; i++)
+ {
+ seqs[i] = seqsel.getSequenceAt(i).getName();
+ }
+ if (strt < seqsel.getStartRes())
+ {
+ strt = seqsel.getStartRes();
+ }
+ if (end == -1 || end > seqsel.getEndRes())
+ {
+ end = seqsel.getEndRes();
+ }
+ }
+ if (colsel != null && !colsel.isEmpty())
+ {
+ if (end == -1)
+ {
+ end = colsel.getMax() + 1;
+ }
+ cols = new String[colsel.getSelected().size()];
+ for (int i = 0; i < cols.length; i++)
+ {
+ cols[i] = "" + (1 + colsel.getSelected().get(i).intValue());
+ }
+ }
+ else
+ {
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ // send a valid range, otherwise we send the empty selection
+ cols = new String[2];
+ cols[0] = "" + (1 + strt) + "-" + (1 + end);
+ }
+ }
+ return new Object[]
+ { src, setid, arrayToSeparatorList(seqs), arrayToSeparatorList(cols) };
+ }
+
+ @Override
+ public String getJsMessage(String messageclass, String viewId)
+ {
+ return JSFunctionExec.getJsMessage(messageclass, viewId, this);
+ }
+
+ @Override
+ public Object getFrameForSource(VamsasSource source)
+ {
+ if (source != null)
+ {
+ if (source instanceof jalview.appletgui.AlignViewport
+ && ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame.viewport == source)
+ {
+ // should be valid if it just generated an event!
+ return ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame;
+
+ }
+ // TODO: ensure that if '_af' is specified along with a handler
+ // function, then only events from that alignFrame are sent to that
+ // function
+ }
+ return null;
+ }
+
+ @Override
+ public FeatureRenderer getNewFeatureRenderer(AlignViewportI vp)
+ {
+ return new jalview.appletgui.FeatureRenderer((AlignmentViewport) vp);
+ }
+
+ @Override
+ public String getSelectedSequencesAsAlignment(String format,
+ boolean suffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+ String format, boolean suffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ // /**
+ // * bind structures in a viewer to any matching sequences in an alignFrame
+ // (use
+ // * sequenceIds to limit scope of search to specific sequences)
+ // *
+ // * @param alFrame
+ // * @param viewer
+ // * @param sequenceIds
+ // * @return TODO: consider making an exception structure for indicating when
+ // * binding fails public SequenceStructureBinding
+ // * addStructureViewInstance( AlignFrame alFrame, Object viewer, String
+ // * sequenceIds) {
+ // *
+ // * if (sequenceIds != null && sequenceIds.length() > 0) { return
+ // * alFrame.addStructureViewInstance(viewer,
+ // * separatorListToArray(sequenceIds)); } else { return
+ // * alFrame.addStructureViewInstance(viewer, null); } // return null; }
+ // */
}
import jalview.datamodel.SequenceFeature;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import intervalstore.api.IntervalStoreI;
import intervalstore.impl.BinarySearcher;
-import intervalstore.impl.IntervalStore;
+import intervalstore.impl.BinarySearcher.Compare;
-/**
- * A data store for a set of sequence features that supports efficient lookup of
- * features overlapping a given range. Intended for (but not limited to) storage
- * of features for one sequence and feature type.
- *
- * @author gmcarstairs
- *
- */
public class FeatureStore
{
+ public enum IntervalStoreType
+ {
+ /**
+ * original NCList-based IntervalStore
+ */
+ INTERVAL_STORE_NCLIST,
+
+ /**
+ * linked-list IntervalStore
+ */
+ INTERVAL_STORE_LINKED_LIST,
+
+ /**
+ * NCList as array buffer IntervalStore
+ */
+ INTERVAL_STORE_NCARRAY
+ }
+
+ /*
+ * track largest start for quick insertion of ordered features
+ */
+ protected int maxStart = -1;
+
+ protected int maxContactStart = -1;
+
/*
* Non-positional features have no (zero) start/end position.
* Kept as a separate list in case this criterion changes in future.
float nonPositionalMaxScore;
/**
- * Constructor
+ * Answers the 'length' of the feature, counting 0 for non-positional features
+ * and 1 for contact features
+ *
+ * @param feature
+ * @return
*/
- public FeatureStore()
+ protected static int getFeatureLength(SequenceFeature feature)
{
- features = new IntervalStore<>();
- positionalFeatureGroups = new HashSet<>();
- nonPositionalFeatureGroups = new HashSet<>();
- positionalMinScore = Float.NaN;
- positionalMaxScore = Float.NaN;
- nonPositionalMinScore = Float.NaN;
- nonPositionalMaxScore = Float.NaN;
-
- // we only construct nonPositionalFeatures, contactFeatures if we need to
+ if (feature.isNonPositional())
+ {
+ return 0;
+ }
+ if (feature.isContactFeature())
+ {
+ return 1;
+ }
+ return 1 + feature.getEnd() - feature.getBegin();
}
/**
- * Adds one sequence feature to the store, and returns true, unless the
- * feature is already contained in the store, in which case this method
- * returns false. Containment is determined by SequenceFeature.equals()
- * comparison.
+ * Answers true if the list contains the feature, else false. This method is
+ * optimised for the condition that the list is sorted on feature start
+ * position ascending, and will give unreliable results if this does not hold.
*
+ * @param list
* @param feature
+ * @return
*/
- public boolean addFeature(SequenceFeature feature)
+ public static boolean listContains(List<SequenceFeature> list,
+ SequenceFeature feature)
{
- if (contains(feature))
+ if (list == null || feature == null)
{
return false;
}
/*
- * keep a record of feature groups
- */
- if (!feature.isNonPositional())
- {
- positionalFeatureGroups.add(feature.getFeatureGroup());
- }
-
- if (feature.isContactFeature())
- {
- addContactFeature(feature);
- }
- else if (feature.isNonPositional())
- {
- addNonPositionalFeature(feature);
- }
- else
- {
- addNestedFeature(feature);
- }
-
- /*
- * record the total extent of positional features, to make
- * getTotalFeatureLength possible; we count the length of a
- * contact feature as 1
- */
- totalExtent += getFeatureLength(feature);
-
- /*
- * record the minimum and maximum score for positional
- * and non-positional features
+ * locate the first entry in the list which does not precede the feature
*/
- float score = feature.getScore();
- if (!Float.isNaN(score))
+ int begin = feature.begin;
+ int pos = BinarySearcher.findFirst(list, true, Compare.GE, begin);
+ int len = list.size();
+ while (pos < len)
{
- if (feature.isNonPositional())
+ SequenceFeature sf = list.get(pos);
+ if (sf.begin > begin)
{
- nonPositionalMinScore = min(nonPositionalMinScore, score);
- nonPositionalMaxScore = max(nonPositionalMaxScore, score);
+ return false; // no match found
}
- else
+ if (sf.equals(feature))
{
- positionalMinScore = min(positionalMinScore, score);
- positionalMaxScore = max(positionalMaxScore, score);
+ return true;
}
+ pos++;
}
-
- return true;
+ return false;
}
/**
- * Answers true if this store contains the given feature (testing by
- * SequenceFeature.equals), else false
+ * A helper method to return the maximum of two floats, where a non-NaN value
+ * is treated as 'greater than' a NaN value (unlike Math.max which does the
+ * opposite)
*
- * @param feature
- * @return
+ * @param f1
+ * @param f2
*/
- public boolean contains(SequenceFeature feature)
+ protected static float max(float f1, float f2)
{
- if (feature.isNonPositional())
+ if (Float.isNaN(f1))
{
- return nonPositionalFeatures == null ? false : nonPositionalFeatures
- .contains(feature);
+ return Float.isNaN(f2) ? f1 : f2;
}
-
- if (feature.isContactFeature())
+ else
{
- return contactFeatureStarts == null ? false : listContains(
- contactFeatureStarts, feature);
+ return Float.isNaN(f2) ? f1 : Math.max(f1, f2);
}
-
- return features == null ? false : features
- .contains(feature);
}
/**
- * Answers the 'length' of the feature, counting 0 for non-positional features
- * and 1 for contact features
+ * A helper method to return the minimum of two floats, where a non-NaN value
+ * is treated as 'less than' a NaN value (unlike Math.min which does the
+ * opposite)
*
- * @param feature
- * @return
+ * @param f1
+ * @param f2
*/
- protected static int getFeatureLength(SequenceFeature feature)
+ protected static float min(float f1, float f2)
{
- if (feature.isNonPositional())
+ if (Float.isNaN(f1))
{
- return 0;
+ return Float.isNaN(f2) ? f1 : f2;
}
- if (feature.isContactFeature())
+ else
{
- return 1;
+ return Float.isNaN(f2) ? f1 : Math.min(f1, f2);
}
- return 1 + feature.getEnd() - feature.getBegin();
}
/**
- * Adds the feature to the list of non-positional features (with lazy
- * instantiation of the list if it is null), and returns true. The feature
- * group is added to the set of distinct feature groups for non-positional
- * features. This method allows duplicate features, so test before calling to
- * prevent this.
- *
- * @param feature
+ * Constructor that defaults to using NCList IntervalStore
*/
- protected boolean addNonPositionalFeature(SequenceFeature feature)
+ public FeatureStore()
{
- if (nonPositionalFeatures == null)
- {
- nonPositionalFeatures = new ArrayList<>();
- }
-
- nonPositionalFeatures.add(feature);
+ this(IntervalStoreType.INTERVAL_STORE_NCLIST);
+ }
- nonPositionalFeatureGroups.add(feature.getFeatureGroup());
+ /**
+ * Constructor that allows an alternative IntervalStore implementation to be
+ * chosen
+ */
+ public FeatureStore(IntervalStoreType intervalStoreType)
+ {
+ features = getIntervalStore(intervalStoreType);
+ positionalFeatureGroups = new HashSet<>();
+ nonPositionalFeatureGroups = new HashSet<>();
+ positionalMinScore = Float.NaN;
+ positionalMaxScore = Float.NaN;
+ nonPositionalMinScore = Float.NaN;
+ nonPositionalMaxScore = Float.NaN;
- return true;
+ // only construct nonPositionalFeatures or contactFeatures if needed
}
/**
- * Adds one feature to the IntervalStore that can manage nested features
- * (creating the IntervalStore if necessary)
+ * Returns a new instance of IntervalStoreI of implementation as selected by
+ * the type parameter
+ *
+ * @param type
+ * @return
*/
- protected synchronized void addNestedFeature(SequenceFeature feature)
+ private IntervalStoreI<SequenceFeature> getIntervalStore(
+ IntervalStoreType type)
{
- if (features == null)
+ switch (type)
{
- features = new IntervalStore<>();
+ default:
+ case INTERVAL_STORE_NCLIST:
+ return new intervalstore.impl.IntervalStore<>();
+ case INTERVAL_STORE_NCARRAY:
+ return new intervalstore.nonc.IntervalStore<>();
+ case INTERVAL_STORE_LINKED_LIST:
+ return new intervalstore.nonc.IntervalStore0<>();
}
- features.add(feature);
}
/**
if (contactFeatureStarts == null)
{
contactFeatureStarts = new ArrayList<>();
- }
- if (contactFeatureEnds == null)
- {
contactFeatureEnds = new ArrayList<>();
}
* insert into list sorted by start (first contact position):
* binary search the sorted list to find the insertion point
*/
- int insertPosition = BinarySearcher.findFirst(contactFeatureStarts,
- f -> f.getBegin() >= feature.getBegin());
- contactFeatureStarts.add(insertPosition, feature);
-
-
+ int insertAt = BinarySearcher.findFirst(contactFeatureStarts, true,
+ Compare.GE, feature.begin);
+ contactFeatureStarts.add(insertAt, feature);
/*
* insert into list sorted by end (second contact position):
* binary search the sorted list to find the insertion point
*/
- insertPosition = BinarySearcher.findFirst(contactFeatureEnds,
- f -> f.getEnd() >= feature.getEnd());
- contactFeatureEnds.add(insertPosition, feature);
+ contactFeatureEnds.add(findFirstEnd(contactFeatureEnds, feature.end),
+ feature);
return true;
}
/**
- * Answers true if the list contains the feature, else false. This method is
- * optimised for the condition that the list is sorted on feature start
- * position ascending, and will give unreliable results if this does not hold.
+ * Adds one sequence feature to the store, and returns true, unless the
+ * feature is already contained in the store, in which case this method
+ * returns false. Containment is determined by SequenceFeature.equals()
+ * comparison.
*
- * @param features
* @param feature
- * @return
*/
- protected static boolean listContains(List<SequenceFeature> features,
- SequenceFeature feature)
+ public boolean addFeature(SequenceFeature feature)
{
- if (features == null || feature == null)
+ if (feature.isContactFeature())
{
- return false;
+ if (containsContactFeature(feature))
+ {
+ return false;
+ }
+ positionalFeatureGroups.add(feature.getFeatureGroup());
+ if (feature.begin > maxContactStart)
+ {
+ maxContactStart = feature.begin;
+ }
+ addContactFeature(feature);
}
+ else if (feature.isNonPositional())
+ {
+ if (containsNonPositionalFeature(feature))
+ {
+ return false;
+ }
- /*
- * locate the first entry in the list which does not precede the feature
- */
- // int pos = binarySearch(features,
- // SearchCriterion.byFeature(feature, RangeComparator.BY_START_POSITION));
- int pos = BinarySearcher.findFirst(features,
- val -> val.getBegin() >= feature.getBegin());
- int len = features.size();
- while (pos < len)
+ addNonPositionalFeature(feature);
+ }
+ else
{
- SequenceFeature sf = features.get(pos);
- if (sf.getBegin() > feature.getBegin())
+ if (!features.add(feature, false))
{
- return false; // no match found
+ return false;
}
- if (sf.equals(feature))
+ positionalFeatureGroups.add(feature.getFeatureGroup());
+ if (feature.begin > maxStart)
{
- return true;
+ maxStart = feature.begin;
}
- pos++;
}
- return false;
- }
-
- /**
- * Returns a (possibly empty) list of features whose extent overlaps the given
- * range. The returned list is not ordered. Contact features are included if
- * either of the contact points lies within the range.
- *
- * @param start
- * start position of overlap range (inclusive)
- * @param end
- * end position of overlap range (inclusive)
- * @return
- */
- public List<SequenceFeature> findOverlappingFeatures(long start, long end)
- {
- List<SequenceFeature> result = new ArrayList<>();
- findContactFeatures(start, end, result);
+ /*
+ * record the total extent of positional features, to make
+ * getTotalFeatureLength possible; we count the length of a
+ * contact feature as 1
+ */
+ totalExtent += getFeatureLength(feature);
- if (features != null)
+ /*
+ * record the minimum and maximum score for positional
+ * and non-positional features
+ */
+ float score = feature.getScore();
+ if (!Float.isNaN(score))
{
- result.addAll(features.findOverlaps(start, end));
+ if (feature.isNonPositional())
+ {
+ nonPositionalMinScore = min(nonPositionalMinScore, score);
+ nonPositionalMaxScore = max(nonPositionalMaxScore, score);
+ }
+ else
+ {
+ positionalMinScore = min(positionalMinScore, score);
+ positionalMaxScore = max(positionalMaxScore, score);
+ }
}
- return result;
+ return true;
}
/**
- * Adds contact features to the result list where either the second or the
- * first contact position lies within the target range
+ * A helper method that adds to the result list any features from the
+ * collection provided whose feature group matches the specified group
*
- * @param from
- * @param to
+ * @param group
+ * @param sfs
* @param result
*/
- protected void findContactFeatures(long from, long to,
- List<SequenceFeature> result)
+ private void addFeaturesForGroup(String group,
+ Collection<SequenceFeature> sfs, List<SequenceFeature> result)
{
- if (contactFeatureStarts != null)
+ if (sfs == null)
{
- findContactStartOverlaps(from, to, result);
+ return;
}
- if (contactFeatureEnds != null)
+ for (SequenceFeature sf : sfs)
{
- findContactEndOverlaps(from, to, result);
+ String featureGroup = sf.getFeatureGroup();
+ if (group == null && featureGroup == null
+ || group != null && group.equals(featureGroup))
+ {
+ result.add(sf);
+ }
}
}
/**
- * Adds to the result list any contact features whose end (second contact
- * point), but not start (first contact point), lies in the query from-to
- * range
+ * Adds the feature to the list of non-positional features (with lazy
+ * instantiation of the list if it is null), and returns true. The feature
+ * group is added to the set of distinct feature groups for non-positional
+ * features. This method allows duplicate features, so test before calling to
+ * prevent this.
*
- * @param from
- * @param to
- * @param result
+ * @param feature
*/
- protected void findContactEndOverlaps(long from, long to,
- List<SequenceFeature> result)
+ protected boolean addNonPositionalFeature(SequenceFeature feature)
{
- /*
- * find the first contact feature (if any)
- * whose end point is not before the target range
- */
- int index = BinarySearcher.findFirst(contactFeatureEnds,
- f -> f.getEnd() >= from);
-
- while (index < contactFeatureEnds.size())
+ if (nonPositionalFeatures == null)
{
- SequenceFeature sf = contactFeatureEnds.get(index);
- if (!sf.isContactFeature())
- {
- System.err.println("Error! non-contact feature type "
- + sf.getType() + " in contact features list");
- index++;
- continue;
- }
-
- int begin = sf.getBegin();
- if (begin >= from && begin <= to)
- {
- /*
- * this feature's first contact position lies in the search range
- * so we don't include it in results a second time
- */
- index++;
- continue;
- }
-
- if (sf.getEnd() > to)
- {
- /*
- * this feature (and all following) has end point after the target range
- */
- break;
- }
-
- /*
- * feature has end >= from and end <= to
- * i.e. contact end point lies within overlap search range
- */
- result.add(sf);
- index++;
+ nonPositionalFeatures = new ArrayList<>();
}
- }
- /**
- * Adds contact features whose start position lies in the from-to range to the
- * result list
- *
- * @param from
- * @param to
- * @param result
- */
- protected void findContactStartOverlaps(long from, long to,
- List<SequenceFeature> result)
- {
- int index = BinarySearcher.findFirst(contactFeatureStarts,
- f -> f.getBegin() >= from);
+ nonPositionalFeatures.add(feature);
- while (index < contactFeatureStarts.size())
- {
- SequenceFeature sf = contactFeatureStarts.get(index);
- if (!sf.isContactFeature())
- {
- System.err.println("Error! non-contact feature " + sf.toString()
- + " in contact features list");
- index++;
- continue;
- }
- if (sf.getBegin() > to)
- {
- /*
- * this feature's start (and all following) follows the target range
- */
- break;
- }
+ nonPositionalFeatureGroups.add(feature.getFeatureGroup());
- /*
- * feature has begin >= from and begin <= to
- * i.e. contact start point lies within overlap search range
- */
- result.add(sf);
- index++;
- }
+ return true;
}
/**
- * Answers a list of all positional features stored, in no guaranteed order
+ * Answers true if this store contains the given feature (testing by
+ * SequenceFeature.equals), else false
*
+ * @param feature
* @return
*/
- public List<SequenceFeature> getPositionalFeatures()
+ public boolean contains(SequenceFeature feature)
{
- List<SequenceFeature> result = new ArrayList<>();
-
- /*
- * add any contact features - from the list by start position
- */
- if (contactFeatureStarts != null)
+ if (feature.isNonPositional())
{
- result.addAll(contactFeatureStarts);
+ return containsNonPositionalFeature(feature);
}
- /*
- * add any nested features
- */
- if (features != null)
+ if (feature.isContactFeature())
{
- result.addAll(features);
+ return containsContactFeature(feature);
}
- return result;
+ return containsPositionalFeature(feature);
+ }
+
+ private boolean containsPositionalFeature(SequenceFeature feature)
+ {
+ return features == null || feature.begin > maxStart ? false
+ : features.contains(feature);
}
/**
- * Answers a list of all contact features. If there are none, returns an
- * immutable empty list.
+ * Answers true if this store already contains a contact feature equal to the
+ * given feature (by {@code SequenceFeature.equals()} test), else false
*
+ * @param feature
* @return
*/
- public List<SequenceFeature> getContactFeatures()
+ private boolean containsContactFeature(SequenceFeature feature)
{
- if (contactFeatureStarts == null)
- {
- return Collections.emptyList();
- }
- return new ArrayList<>(contactFeatureStarts);
+ return contactFeatureStarts != null && feature.begin <= maxContactStart
+ && listContains(contactFeatureStarts, feature);
}
/**
- * Answers a list of all non-positional features. If there are none, returns
- * an immutable empty list.
+ * Answers true if this store already contains a non-positional feature equal
+ * to the given feature (by {@code SequenceFeature.equals()} test), else false
*
+ * @param feature
* @return
*/
- public List<SequenceFeature> getNonPositionalFeatures()
+ private boolean containsNonPositionalFeature(SequenceFeature feature)
{
- if (nonPositionalFeatures == null)
- {
- return Collections.emptyList();
- }
- return new ArrayList<>(nonPositionalFeatures);
+ return nonPositionalFeatures == null ? false
+ : nonPositionalFeatures.contains(feature);
}
/**
}
}
- boolean removedNonPositional = false;
-
/*
* if not found, try non-positional features
*/
if (!removed && nonPositionalFeatures != null)
{
- removedNonPositional = nonPositionalFeatures.remove(sf);
- removed = removedNonPositional;
+ removed = nonPositionalFeatures.remove(sf);
}
/*
return removed;
}
+ public List<SequenceFeature> findFeatures(long start, long end)
+ {
+ return findFeatures(start, end, null);
+ }
+
/**
- * Rescan all features to recompute any cached values after an entry has been
- * deleted. This is expected to be an infrequent event, so performance here is
- * not critical.
+ * Returns a (possibly empty) list of features whose extent overlaps the given
+ * range. The returned list is not ordered. Contact features are included if
+ * either of the contact points lies within the range. If the {@code result}
+ * parameter is not null, new entries are added to this list and the (possibly
+ * extended) list returned.
+ *
+ * @param start
+ * start position of overlap range (inclusive)
+ * @param end
+ * end position of overlap range (inclusive)
+ * @param result
+ * @return
*/
- protected synchronized void rescanAfterDelete()
+ public List<SequenceFeature> findFeatures(long start, long end,
+ List<SequenceFeature> result)
{
- positionalFeatureGroups.clear();
- nonPositionalFeatureGroups.clear();
- totalExtent = 0;
- positionalMinScore = Float.NaN;
- positionalMaxScore = Float.NaN;
- nonPositionalMinScore = Float.NaN;
- nonPositionalMaxScore = Float.NaN;
-
- /*
- * scan non-positional features for groups and scores
- */
- for (SequenceFeature sf : getNonPositionalFeatures())
+ if (result == null)
{
- nonPositionalFeatureGroups.add(sf.getFeatureGroup());
- float score = sf.getScore();
- nonPositionalMinScore = min(nonPositionalMinScore, score);
- nonPositionalMaxScore = max(nonPositionalMaxScore, score);
+ result = new ArrayList<>();
}
- /*
- * scan positional features for groups, scores and extents
- */
- for (SequenceFeature sf : getPositionalFeatures())
- {
- positionalFeatureGroups.add(sf.getFeatureGroup());
- float score = sf.getScore();
- positionalMinScore = min(positionalMinScore, score);
- positionalMaxScore = max(positionalMaxScore, score);
- totalExtent += getFeatureLength(sf);
- }
+ findContactFeatures(start, end, result);
+ features.findOverlaps(start, end, result);
+
+ return result;
}
/**
- * A helper method to return the minimum of two floats, where a non-NaN value
- * is treated as 'less than' a NaN value (unlike Math.min which does the
- * opposite)
+ * Returns a (possibly empty) list of stored contact features
*
- * @param f1
- * @param f2
+ * @return
*/
- protected static float min(float f1, float f2)
+ public List<SequenceFeature> getContactFeatures()
{
- if (Float.isNaN(f1))
- {
- return Float.isNaN(f2) ? f1 : f2;
- }
- else
- {
- return Float.isNaN(f2) ? f1 : Math.min(f1, f2);
- }
+ List<SequenceFeature> result = new ArrayList<>();
+ getContactFeatures(result);
+ return result;
}
/**
- * A helper method to return the maximum of two floats, where a non-NaN value
- * is treated as 'greater than' a NaN value (unlike Math.max which does the
- * opposite)
+ * Adds any stored contact features to the result list
*
- * @param f1
- * @param f2
+ * @return
*/
- protected static float max(float f1, float f2)
+ public void getContactFeatures(List<SequenceFeature> result)
{
- if (Float.isNaN(f1))
- {
- return Float.isNaN(f2) ? f1 : f2;
- }
- else
+ if (contactFeatureStarts != null)
{
- return Float.isNaN(f2) ? f1 : Math.max(f1, f2);
+ result.addAll(contactFeatureStarts);
}
}
/**
- * Answers true if this store has no features, else false
+ * Answers the number of positional (or non-positional) features stored.
+ * Contact features count as 1.
*
+ * @param positional
* @return
*/
- public boolean isEmpty()
+ public int getFeatureCount(boolean positional)
{
- boolean hasFeatures = (contactFeatureStarts != null
- && !contactFeatureStarts
- .isEmpty())
- || (nonPositionalFeatures != null && !nonPositionalFeatures
- .isEmpty())
- || (features != null && features.size() > 0);
+ if (!positional)
+ {
+ return nonPositionalFeatures == null ? 0
+ : nonPositionalFeatures.size();
+ }
- return !hasFeatures;
+ int size = 0;
+
+ if (contactFeatureStarts != null)
+ {
+ // note a contact feature (start/end) counts as one
+ size += contactFeatureStarts.size();
+ }
+
+ if (features != null)
+ {
+ size += features.size();
+ }
+ return size;
}
/**
}
else
{
- return nonPositionalFeatureGroups == null ? Collections
- .<String> emptySet() : Collections
- .unmodifiableSet(nonPositionalFeatureGroups);
+ return nonPositionalFeatureGroups == null
+ ? Collections.<String> emptySet()
+ : Collections.unmodifiableSet(nonPositionalFeatureGroups);
}
}
/**
- * Answers the number of positional (or non-positional) features stored.
- * Contact features count as 1.
+ * Answers a list of all either positional or non-positional features whose
+ * feature group matches the given group (which may be null)
*
* @param positional
+ * @param group
* @return
*/
- public int getFeatureCount(boolean positional)
+ public List<SequenceFeature> getFeaturesForGroup(boolean positional,
+ String group)
{
- if (!positional)
+ List<SequenceFeature> result = new ArrayList<>();
+
+ /*
+ * if we know features don't include the target group, no need
+ * to inspect them for matches
+ */
+ if (positional && !positionalFeatureGroups.contains(group)
+ || !positional && !nonPositionalFeatureGroups.contains(group))
{
- return nonPositionalFeatures == null ? 0 : nonPositionalFeatures
- .size();
+ return result;
}
- int size = 0;
-
- if (contactFeatureStarts != null)
+ if (positional)
{
- // note a contact feature (start/end) counts as one
- size += contactFeatureStarts.size();
+ addFeaturesForGroup(group, contactFeatureStarts, result);
+ addFeaturesForGroup(group, features, result);
}
-
- if (features != null)
+ else
{
- size += features.size();
+ addFeaturesForGroup(group, nonPositionalFeatures, result);
}
-
- return size;
+ return result;
}
/**
- * Answers the total length of positional features (or zero if there are
- * none). Contact features contribute a value of 1 to the total.
+ * Answers the maximum score held for positional or non-positional features.
+ * This may be Float.NaN if there are no features, are none has a non-NaN
+ * score.
*
+ * @param positional
* @return
*/
- public int getTotalFeatureLength()
+ public float getMaximumScore(boolean positional)
{
- return totalExtent;
+ return positional ? positionalMaxScore : nonPositionalMaxScore;
}
/**
}
/**
- * Answers the maximum score held for positional or non-positional features.
- * This may be Float.NaN if there are no features, are none has a non-NaN
- * score.
+ * Answers a (possibly empty) list of all non-positional features
*
- * @param positional
* @return
*/
- public float getMaximumScore(boolean positional)
+ public List<SequenceFeature> getNonPositionalFeatures()
{
- return positional ? positionalMaxScore : nonPositionalMaxScore;
+ List<SequenceFeature> result = new ArrayList<>();
+ getNonPositionalFeatures(result);
+ return result;
}
/**
- * Answers a list of all either positional or non-positional features whose
- * feature group matches the given group (which may be null)
+ * Adds any stored non-positional features to the result list
*
- * @param positional
- * @param group
* @return
*/
- public List<SequenceFeature> getFeaturesForGroup(boolean positional,
- String group)
+ public void getNonPositionalFeatures(List<SequenceFeature> result)
+ {
+ if (nonPositionalFeatures != null)
+ {
+ result.addAll(nonPositionalFeatures);
+ }
+ }
+
+ /**
+ * Returns a (possibly empty) list of all positional features stored
+ *
+ * @return
+ */
+ public List<SequenceFeature> getPositionalFeatures()
{
List<SequenceFeature> result = new ArrayList<>();
+ getPositionalFeatures(result);
+
+ return result;
+ }
+ /**
+ * Adds all positional features stored to the result list, in no guaranteed
+ * order, and with no check for duplicates
+ */
+ public void getPositionalFeatures(List<SequenceFeature> result)
+ {
/*
- * if we know features don't include the target group, no need
- * to inspect them for matches
+ * add any contact features - from the list by start position
*/
- if (positional && !positionalFeatureGroups.contains(group)
- || !positional && !nonPositionalFeatureGroups.contains(group))
+ if (contactFeatureStarts != null)
{
- return result;
+ result.addAll(contactFeatureStarts);
}
- List<SequenceFeature> sfs = positional ? getPositionalFeatures()
- : getNonPositionalFeatures();
- for (SequenceFeature sf : sfs)
+ /*
+ * add any nested features
+ */
+ if (features != null)
{
- String featureGroup = sf.getFeatureGroup();
- if (group == null && featureGroup == null || group != null
- && group.equals(featureGroup))
+ result.addAll(features);
+ }
+ }
+
+ /**
+ * Answers the total length of positional features (or zero if there are
+ * none). Contact features contribute a value of 1 to the total.
+ *
+ * @return
+ */
+ public int getTotalFeatureLength()
+ {
+ return totalExtent;
+ }
+
+ /**
+ * Answers true if this store has no features, else false
+ *
+ * @return
+ */
+ public boolean isEmpty()
+ {
+ boolean hasFeatures = (contactFeatureStarts != null
+ && !contactFeatureStarts.isEmpty())
+ || (nonPositionalFeatures != null
+ && !nonPositionalFeatures.isEmpty())
+ || (features != null && features.size() > 0);
+
+ return !hasFeatures;
+ }
+
+ /**
+ * Rescan all features to recompute any cached values after an entry has been
+ * deleted. This is expected to be an infrequent event, so performance here is
+ * not critical.
+ */
+ protected synchronized void rescanAfterDelete()
+ {
+ positionalFeatureGroups.clear();
+ nonPositionalFeatureGroups.clear();
+ totalExtent = 0;
+ positionalMinScore = Float.NaN;
+ positionalMaxScore = Float.NaN;
+ nonPositionalMinScore = Float.NaN;
+ nonPositionalMaxScore = Float.NaN;
+ /*
+ * scan non-positional features for groups and scores
+ */
+ if (nonPositionalFeatures != null)
+ {
+ for (int i = 0, n = nonPositionalFeatures.size(); i < n; i++)
{
- result.add(sf);
+ SequenceFeature sf = nonPositionalFeatures.get(i);
+ nonPositionalFeatureGroups.add(sf.getFeatureGroup());
+ float score = sf.getScore();
+ nonPositionalMinScore = min(nonPositionalMinScore, score);
+ nonPositionalMaxScore = max(nonPositionalMaxScore, score);
}
}
- return result;
+
+ rescanPositional(contactFeatureStarts);
+ rescanPositional(features);
+ }
+
+ /**
+ * Scans the given features and updates cached feature groups, minimum and
+ * maximum feature score, and total feature extent (length) for positional
+ * features
+ *
+ * @param sfs
+ */
+ private void rescanPositional(Collection<SequenceFeature> sfs)
+ {
+ if (sfs == null)
+ {
+ return;
+ }
+ for (SequenceFeature sf : sfs)
+ {
+ positionalFeatureGroups.add(sf.getFeatureGroup());
+ float score = sf.getScore();
+ positionalMinScore = min(positionalMinScore, score);
+ positionalMaxScore = max(positionalMaxScore, score);
+ totalExtent += getFeatureLength(sf);
+ }
}
/**
* (Although a simple shift of all values would preserve data integrity!)
*/
boolean modified = false;
- for (SequenceFeature sf : getPositionalFeatures())
+ List<SequenceFeature> list = getPositionalFeatures();
+ for (int i = 0, n = list.size(); i < n; i++)
{
+ SequenceFeature sf = list.get(i);
if (sf.getBegin() >= fromPosition)
{
modified = true;
}
return modified;
}
+
+ /**
+ * Answers the position (0, 1...) in the list of the first entry whose end
+ * position is not less than {@ pos}. If no such entry is found, answers the
+ * length of the list.
+ *
+ * @param list
+ * @param pos
+ * @return
+ */
+ protected int findFirstEnd(List<SequenceFeature> list, long pos)
+ {
+ return BinarySearcher.findFirst(list, false, Compare.GE, (int) pos);
+ }
+
+ /**
+ * Adds contact features to the result list where either the second or the
+ * first contact position lies within the target range
+ *
+ * @param from
+ * @param to
+ * @param result
+ */
+ protected void findContactFeatures(long from, long to,
+ List<SequenceFeature> result)
+ {
+ if (contactFeatureStarts != null)
+ {
+ findContactStartOverlaps(from, to, result);
+ findContactEndOverlaps(from, to, result);
+ }
+ }
+
+ /**
+ * Adds to the result list any contact features whose end (second contact
+ * point), but not start (first contact point), lies in the query from-to
+ * range
+ *
+ * @param from
+ * @param to
+ * @param result
+ */
+ private void findContactEndOverlaps(long from, long to,
+ List<SequenceFeature> result)
+ {
+ /*
+ * find the first contact feature (if any)
+ * whose end point is not before the target range
+ */
+ int index = findFirstEnd(contactFeatureEnds, from);
+
+ int n = contactFeatureEnds.size();
+ while (index < n)
+ {
+ SequenceFeature sf = contactFeatureEnds.get(index);
+ if (!sf.isContactFeature())
+ {
+ System.err.println("Error! non-contact feature type " + sf.getType()
+ + " in contact features list");
+ index++;
+ continue;
+ }
+
+ int begin = sf.getBegin();
+ if (begin >= from && begin <= to)
+ {
+ /*
+ * this feature's first contact position lies in the search range
+ * so we don't include it in results a second time
+ */
+ index++;
+ continue;
+ }
+
+ if (sf.getEnd() > to)
+ {
+ /*
+ * this feature (and all following) has end point after the target range
+ */
+ break;
+ }
+
+ /*
+ * feature has end >= from and end <= to
+ * i.e. contact end point lies within overlap search range
+ */
+ result.add(sf);
+ index++;
+ }
+ }
+
+ /**
+ * Adds contact features whose start position lies in the from-to range to the
+ * result list
+ *
+ * @param from
+ * @param to
+ * @param result
+ */
+ private void findContactStartOverlaps(long from, long to,
+ List<SequenceFeature> result)
+ {
+ int index = BinarySearcher.findFirst(contactFeatureStarts, true,
+ Compare.GE, (int) from);
+
+ while (index < contactFeatureStarts.size())
+ {
+ SequenceFeature sf = contactFeatureStarts.get(index);
+ if (!sf.isContactFeature())
+ {
+ System.err.println("Error! non-contact feature " + sf.toString()
+ + " in contact features list");
+ index++;
+ continue;
+ }
+ if (sf.getBegin() > to)
+ {
+ /*
+ * this feature's start (and all following) follows the target range
+ */
+ break;
+ }
+
+ /*
+ * feature has begin >= from and begin <= to
+ * i.e. contact start point lies within overlap search range
+ */
+ result.add(sf);
+ index++;
+ }
+ }
+
}
import jalview.datamodel.SequenceFeature;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
+import jalview.util.Platform;
import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
*/
public class SequenceFeatures implements SequenceFeaturesI
{
-
/*
* map from feature type to structured store of features for that type
* null types are permitted (but not a good idea!)
String... type)
{
List<SequenceFeature> result = new ArrayList<>();
-
for (FeatureStore featureSet : varargToTypes(type))
{
- result.addAll(featureSet.findOverlappingFeatures(from, to));
+ // BH MUCH more efficient to pass the list
+ featureSet.findFeatures(from, to, result);
}
-
return result;
}
for (FeatureStore featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getPositionalFeatures());
+ featureSet.getPositionalFeatures(result);
}
return result;
}
for (FeatureStore featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getContactFeatures());
+ featureSet.getContactFeatures(result);
}
return result;
}
for (FeatureStore featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getNonPositionalFeatures());
+ featureSet.getNonPositionalFeatures(result);
}
return result;
}
public Set<String> getFeatureGroups(boolean positionalFeatures,
String... type)
{
- Set<String> groups = new HashSet<>();
+ // BH 2020.03.21 This is the set that orders the list of groups
+ // at the top of the FeatureSettings panel.
+ // In order to keep the same order as a Java HashSet, we must
+ // request that specifically. See Platform.
+ Set<String> groups = Platform.getJavaOrderedHashSet();
for (FeatureStore featureSet : varargToTypes(type))
{
public Set<String> getFeatureTypesForGroups(boolean positionalFeatures,
String... groups)
{
- Set<String> result = new HashSet<>();
+ // BH 2020.03.21 This set is the one that sets the initial ordering for
+ // feature rendering. We set it to new HashSet<>(16,0.75) to force it to
+ // be backed by a Java hash-ordered HashMap instead of a JavaScript Map.
+ Set<String> result = Platform.getJavaOrderedHashSet();
for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
{
@Override
public Set<String> getFeatureTypes(String... soTerm)
{
- Set<String> types = new HashSet<>();
+ Set<String> types = Platform.getJavaOrderedHashSet();
for (Entry<String, FeatureStore> entry : featureStore.entrySet())
{
String type = entry.getKey();
{
return true;
}
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
for (String term : soTerm)
{
if (type.equals(term) || so.isA(type, term))
{
featureStore.clear();
}
+
+ @Override
+ public List<SequenceFeature> findFeatures(int pos, String type,
+ List<SequenceFeature> list)
+ {
+ FeatureStore fs = featureStore.get(type);
+ if (fs == null)
+ {
+ return list == null ? new ArrayList<>() : list;
+ }
+ return fs.findFeatures(pos, pos, list);
+ }
+
+ @Override
+ public boolean hasFeatures(String type)
+ {
+ return featureStore.containsKey(type)
+ && !featureStore.get(type).isEmpty();
+ }
+
}
/**
* Returns a (possibly empty) list of features, optionally restricted to
* specified types, which overlap the given (inclusive) sequence position
- * range. If types are specified, features are returned in the order of the
- * types given.
+ * range
*
* @param from
* @param to
* Deletes all positional and non-positional features
*/
void deleteAll();
+
+ /**
+ * Answers a (possibly empty) list of features of the specified type that
+ * overlap the specified column position. If parameter {@code result} is not
+ * null, features are appended to it and the (possibly extended) list is
+ * returned.
+ *
+ * @param pos
+ * @param type
+ * @param result
+ * @return
+ */
+ List<SequenceFeature> findFeatures(int pos, String type, List<SequenceFeature> result);
+
+ /**
+ * Answers true if there are any features of the given type, else false
+ */
+ boolean hasFeatures(String type);
}
@Override
protected boolean retainFeature(SequenceFeature sf, String accessionId)
{
- if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
+ if (SequenceOntologyFactory.getSequenceOntology().isA(sf.getType(),
SequenceOntologyI.CDS))
{
return false;
@Override
protected boolean retainFeature(SequenceFeature sf, String accessionId)
{
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
String type = sf.getType();
if (so.isA(type, SequenceOntologyI.GENE))
{
{
return new FeatureSettingsAdapter()
{
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
@Override
public boolean isFeatureDisplayed(String type)
* for sequence_variant on reverse strand, have to convert the allele
* values to their complements
*/
- if (!forwardStrand && SequenceOntologyFactory.getInstance()
+ if (!forwardStrand && SequenceOntologyFactory.getSequenceOntology()
.isA(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT))
{
reverseComplementAlleles(copy);
public static boolean isTranscript(String featureType)
{
return SequenceOntologyI.NMD_TRANSCRIPT_VARIANT.equals(featureType)
- || SequenceOntologyFactory.getInstance().isA(featureType,
+ || SequenceOntologyFactory.getSequenceOntology().isA(featureType,
SequenceOntologyI.TRANSCRIPT);
}
}
public APQHandlers() {
}
- protected static boolean setAPQHandlers(jalview.gui.Desktop jalviewDesktop)
+ protected boolean setAPQHandlers(jalview.gui.Desktop jalviewDesktop)
{
// flagging this test to avoid unnecessary reflection
if (!setAPQHandlers)
this.settings = defaults;
this.isComplexAlignFile = format.isComplexAlignFile();
init(viewport.hasHiddenRows(), viewport.hasHiddenColumns());
- dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
+ dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane());
}
/**
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
+import java.awt.Dimension;
import java.awt.Rectangle;
import java.awt.Toolkit;
import java.awt.datatransfer.Clipboard;
import java.awt.print.PageFormat;
import java.awt.print.PrinterJob;
import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
import java.io.File;
import java.io.FileWriter;
import java.io.PrintWriter;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
import jalview.api.AlignExportSettingsI;
+import jalview.api.AlignFrameI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
* @version $Revision$
*/
@SuppressWarnings("serial")
-public class AlignFrame extends GAlignFrame implements DropTargetListener,
+public class AlignFrame extends GAlignFrame
+ implements AlignFrameI, DropTargetListener,
IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
/**
* Current filename for this alignment
*/
- String fileName = null;
+ private String fileName = null;
- File fileObject;
+ private File fileObject;
/**
* Creates a new AlignFrame object with specific width and height.
}
viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
+ // BH! new alignPanel must come later
+ // alignPanel = new AlignmentPanel(this, viewport);
+ // addAlignmentPanel(alignPanel, true);
- alignPanel = new AlignmentPanel(this, viewport);
-
- addAlignmentPanel(alignPanel, true);
init();
}
{
viewport.hideSequence(hiddenSeqs);
}
- alignPanel = new AlignmentPanel(this, viewport);
- addAlignmentPanel(alignPanel, true);
- init();
+ // BH! new alignPanel must come later
+ //alignPanel = new AlignmentPanel(this, viewport);
+ //addAlignmentPanel(alignPanel, true);
+init();
}
/**
{
viewport = ap.av;
alignPanel = ap;
- addAlignmentPanel(ap, false);
+ // BH! adding must come later
+ // addAlignmentPanel(ap, false);
init();
}
*/
void init()
{
-// setBackground(Color.white); // BH 2019
-
+ // BH! Here is where we create the panel; note the sequence
+ boolean newPanel = (alignPanel == null);
+ viewport.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+ if (newPanel)
+ {
+ if (Platform.isJS())
+ {
+ // need to set this up front if NOANNOTATION is
+ // used in conjunction with SHOWOVERVIEW.
+
+ // I have not determined if this is appropriate for
+ // Jalview/Java, as it means we are setting this flag
+ // for all subsequent AlignFrames. For now, at least,
+ // I am setting it to be JalviewJS-only.
+
+ boolean showAnnotation = Jalview.getInstance().getShowAnnotation();
+ viewport.setShowAnnotation(showAnnotation);
+ }
+ alignPanel = new AlignmentPanel(this, viewport);
+ }
+ addAlignmentPanel(alignPanel, newPanel);
+
+ // setBackground(Color.white); // BH 2019
+
+ // BH meaning "without display, one way or another"
if (!Jalview.isHeadlessMode())
{
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+ statusPanel.setVisible(Jalview.getInstance().getShowStatus());
+ alignFrameMenuBar.setVisible(Jalview.getInstance().getAllowMenuBar());
}
avc = new jalview.controller.AlignViewController(this, viewport,
// modifyPID.setEnabled(false);
}
- String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
+ String sortby = Cache.getDefault(Preferences.SORT_ALIGNMENT,
"No sort");
if (sortby.equals("Id"))
sortPairwiseMenuItem_actionPerformed(null);
}
- this.alignPanel.av
+ alignPanel.av
.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
setMenusFromViewport(viewport);
});
buildColourMenu();
- if (Desktop.desktop != null)
+ if (Desktop.getDesktopPane() != null)
{
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
if (!Platform.isJS())
wrapMenuItem_actionPerformed(null);
}
- if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+ if (jalview.bin.Cache.getDefault(Preferences.SHOW_OVERVIEW, false))
{
this.overviewMenuItem_actionPerformed(null);
}
switch (evt.getKeyCode())
{
- case 27: // escape key
+ case KeyEvent.VK_ESCAPE: // escape key
deselectAllSequenceMenuItem_actionPerformed(null);
break;
{
ap.av.getAlignment().padGaps();
}
- ap.av.updateConservation(ap);
- ap.av.updateConsensus(ap);
- ap.av.updateStrucConsensus(ap);
+ // BH! important option for JalviewJS
+ if (Jalview.getInstance().getStartCalculations())
+ {
+ ap.av.updateConservation(ap);
+ ap.av.updateConsensus(ap);
+ ap.av.updateStrucConsensus(ap);
+ }
}
}
/* Set up intrinsic listeners for dynamically generated GUI bits. */
private void addServiceListeners()
{
- final java.beans.PropertyChangeListener thisListener;
- Desktop.instance.addJalviewPropertyChangeListener("services",
- thisListener = new java.beans.PropertyChangeListener()
- {
- @Override
- public void propertyChange(PropertyChangeEvent evt)
- {
- // // System.out.println("Discoverer property change.");
- // if (evt.getPropertyName().equals("services"))
- {
- SwingUtilities.invokeLater(new Runnable()
- {
+ PropertyChangeListener thisListener;
+ Desktop.getInstance().addJalviewPropertyChangeListener("services",
+ thisListener = new PropertyChangeListener()
+ {
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
- @Override
- public void run()
- {
+ @Override
+ public void run()
+ {
System.err.println(
"Rebuild WS Menu for service change");
- BuildWebServiceMenu();
- }
-
- });
- }
- }
- });
+ BuildWebServiceMenu();
+ }
+ });
+ }
+ }
+ });
addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
@Override
javax.swing.event.InternalFrameEvent evt)
{
// System.out.println("deregistering discoverer listener");
- Desktop.instance.removeJalviewPropertyChangeListener("services",
+ Desktop.getInstance().removeJalviewPropertyChangeListener("services",
thisListener);
closeMenuItem_actionPerformed(true);
}
scaleLeft.setVisible(av.getWrapAlignment());
scaleRight.setVisible(av.getWrapAlignment());
annotationPanelMenuItem.setState(av.isShowAnnotation());
- /*
- * Show/hide annotations only enabled if annotation panel is shown
- */
- showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
- hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
- showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
- hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ // Show/hide annotations only enabled if annotation panel is shown
+
+ syncAnnotationMenuItems();
+
viewBoxesMenuItem.setSelected(av.getShowBoxes());
viewTextMenuItem.setSelected(av.getShowText());
showNonconservedMenuItem.setSelected(av.getShowUnconserved());
applyToAllGroups.setState(av.getColourAppliesToAllGroups());
showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
showDbRefsMenuitem.setSelected(av.isShowDBRefs());
- autoCalculate.setSelected(av.autoCalculateConsensus);
+ autoCalculate.setSelected(av.getAutoCalculateConsensusAndConservation());
sortByTree.setSelected(av.sortByTree);
listenToViewSelections.setSelected(av.followSelection);
@Override
public void addFromFile_actionPerformed(ActionEvent e)
{
- Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
+ Desktop.getInstance().inputLocalFileMenuItem_actionPerformed(viewport);
}
@Override
public void reload_actionPerformed(ActionEvent e)
{
- if (fileName != null)
+ if (fileName == null)
+ {
+ return;
+ }
+ // TODO: JAL-1108 - ensure all associated frames are closed regardless of
+ // originating file's format
+ // TODO: work out how to recover feature settings for correct view(s) when
+ // file is reloaded.
+ if (FileFormat.Jalview.equals(currentFileFormat))
{
- // TODO: JAL-1108 - ensure all associated frames are closed regardless of
- // originating file's format
- // TODO: work out how to recover feature settings for correct view(s) when
- // file is reloaded.
- if (FileFormat.Jalview.equals(currentFileFormat))
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
+ for (int i = 0; i < frames.length; i++)
{
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- for (int i = 0; i < frames.length; i++)
+ if (frames[i] instanceof AlignFrame && frames[i] != this
+ && ((AlignFrame) frames[i]).fileName != null
+ && ((AlignFrame) frames[i]).fileName.equals(fileName))
{
- if (frames[i] instanceof AlignFrame && frames[i] != this
- && ((AlignFrame) frames[i]).fileName != null
- && ((AlignFrame) frames[i]).fileName.equals(fileName))
+ try
+ {
+ frames[i].setSelected(true);
+ Desktop.getInstance().closeAssociatedWindows();
+ } catch (java.beans.PropertyVetoException ex)
{
- try
- {
- frames[i].setSelected(true);
- Desktop.instance.closeAssociatedWindows();
- } catch (java.beans.PropertyVetoException ex)
- {
- }
}
-
}
- Desktop.instance.closeAssociatedWindows();
- FileLoader loader = new FileLoader();
- DataSourceType protocol = fileName.startsWith("http:")
- ? DataSourceType.URL
- : DataSourceType.FILE;
- loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
}
+ Desktop.getInstance().closeAssociatedWindows();
+
+ FileLoader loader = new FileLoader();
+ DataSourceType protocol = fileName.startsWith("http:")
+ ? DataSourceType.URL
+ : DataSourceType.FILE;
+ if (fileObject == null)
+ loader.LoadFile(fileName, protocol, currentFileFormat);
else
- {
- Rectangle bounds = this.getBounds();
-
- FileLoader loader = new FileLoader();
+ loader.loadFile(null, (File) fileObject, protocol, currentFileFormat);
+ }
+ else
+ {
+ Rectangle bounds = this.getBounds();
- AlignFrame newframe = null;
+ FileLoader loader = new FileLoader();
- if (fileObject == null)
- {
+ AlignFrame newframe = null;
- DataSourceType protocol = (fileName.startsWith("http:")
- ? DataSourceType.URL
- : DataSourceType.FILE);
- newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
- currentFileFormat);
- }
- else
- {
- newframe = loader.LoadFileWaitTillLoaded(fileObject,
- DataSourceType.FILE, currentFileFormat);
- }
+ if (fileObject == null)
+ {
+// BH! Q: What about https?
+ DataSourceType protocol = (fileName.startsWith("http:")
+ ? DataSourceType.URL
+ : DataSourceType.FILE);
+ newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
+ currentFileFormat);
+ }
+ else
+ {
+ newframe = loader.loadFileWaitTillLoaded((File) fileObject,
+ DataSourceType.FILE, currentFileFormat);
+ }
- newframe.setBounds(bounds);
- if (featureSettings != null && featureSettings.isShowing())
+ newframe.setBounds(bounds);
+ if (featureSettings != null && featureSettings.isShowing())
+ {
+ final Rectangle fspos = featureSettings.frame.getBounds();
+ // TODO: need a 'show feature settings' function that takes bounds -
+ // need to refactor Desktop.addFrame
+ newframe.featureSettings_actionPerformed(null);
+ final FeatureSettings nfs = newframe.featureSettings;
+ Jalview.execRunnable(new Runnable()
{
- final Rectangle fspos = featureSettings.frame.getBounds();
- // TODO: need a 'show feature settings' function that takes bounds -
- // need to refactor Desktop.addFrame
- newframe.featureSettings_actionPerformed(null);
- final FeatureSettings nfs = newframe.featureSettings;
- SwingUtilities.invokeLater(new Runnable()
+ @Override
+ public void run()
{
- @Override
- public void run()
- {
- nfs.frame.setBounds(fspos);
- }
- });
- this.featureSettings.close();
- this.featureSettings = null;
- }
- this.closeMenuItem_actionPerformed(true);
+ nfs.frame.setBounds(fspos);
+ }
+ });
+ this.featureSettings.close();
+ this.featureSettings = null;
}
+ this.closeMenuItem_actionPerformed(true);
}
}
@Override
public void addFromText_actionPerformed(ActionEvent e)
{
- Desktop.instance
+ Desktop.getInstance()
.inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
}
@Override
public void addFromURL_actionPerformed(ActionEvent e)
{
- Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
+ Desktop.getInstance().inputURLMenuItem_actionPerformed(viewport);
}
@Override
// todo is this (2005) test now obsolete - value is never null?
while (currentFileFormat == null)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager
.getString("label.select_file_format_before_saving"),
MessageManager.getString("label.file_format_not_specified"),
try
{
String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
- PrintWriter out = new PrintWriter(
+ PrintWriter out = new PrintWriter(
new FileWriter(tempFilePath));
out.print(output);
closeView(alignPanel);
}
}
+
if (closeAllTabs)
{
if (featureSettings != null && featureSettings.isOpen())
StringSelection ss = new StringSelection(output);
+ Desktop d = Desktop.getInstance();
try
{
- jalview.gui.Desktop.internalCopy = true;
+ d.internalCopy = true;
// Its really worth setting the clipboard contents
// to empty before setting the large StringSelection!!
Toolkit.getDefaultToolkit().getSystemClipboard()
.setContents(new StringSelection(""), null);
Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
- Desktop.instance);
+ Desktop.getInstance());
} catch (OutOfMemoryError er)
{
new OOMWarning("copying region", er);
hiddenCutoff, hiddenOffset);
}
- Desktop.jalviewClipboard = new Object[] { seqs,
+ d.jalviewClipboard = new Object[] { seqs,
viewport.getAlignment().getDataset(), hiddenColumns };
setStatus(MessageManager.formatMessage(
"label.copied_sequences_to_clipboard", new Object[]
boolean annotationAdded = false;
AlignmentI alignment = null;
- if (Desktop.jalviewClipboard != null)
+ Desktop d = Desktop.getInstance();
+
+ if (d.jalviewClipboard != null)
{
// The clipboard was filled from within Jalview, we must use the
// sequences
// And dataset from the copied alignment
- SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
+ SequenceI[] newseq = (SequenceI[]) d.jalviewClipboard[0];
// be doubly sure that we create *new* sequence objects.
sequences = new SequenceI[newseq.length];
for (int i = 0; i < newseq.length; i++)
if (newAlignment)
{
- if (Desktop.jalviewClipboard != null)
+ if (d.jalviewClipboard != null)
{
// dataset is inherited
- alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
+ alignment.setDataset((Alignment) d.jalviewClipboard[1]);
}
else
{
alignment = viewport.getAlignment();
alwidth = alignment.getWidth() + 1;
// decide if we need to import sequences from an existing dataset
- boolean importDs = Desktop.jalviewClipboard != null
- && Desktop.jalviewClipboard[1] != alignment.getDataset();
+ boolean importDs = d.jalviewClipboard != null
+ && d.jalviewClipboard[1] != alignment.getDataset();
// importDs==true instructs us to copy over new dataset sequences from
// an existing alignment
Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
DEFAULT_HEIGHT);
String newtitle = new String("Copied sequences");
- if (Desktop.jalviewClipboard != null
- && Desktop.jalviewClipboard[2] != null)
+ if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null)
{
- HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+ HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2];
af.viewport.setHiddenColumns(hc);
}
DEFAULT_HEIGHT);
String newtitle = new String("Flanking alignment");
- if (Desktop.jalviewClipboard != null
- && Desktop.jalviewClipboard[2] != null)
+ Desktop d = Desktop.getInstance();
+
+ if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null)
{
- HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+ HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2];
af.viewport.setHiddenColumns(hc);
}
Runnable okAction = new Runnable()
{
- @Override
- public void run()
- {
- SequenceI[] cut = sg.getSequences()
- .toArray(new SequenceI[sg.getSize()]);
-
- addHistoryItem(new EditCommand(
- MessageManager.getString("label.cut_sequences"), Action.CUT,
- cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
- viewport.getAlignment()));
-
- viewport.setSelectionGroup(null);
- viewport.sendSelection();
- viewport.getAlignment().deleteGroup(sg);
-
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
- if (viewport.getAlignment().getHeight() < 1)
- {
- try
- {
- AlignFrame.this.setClosed(true);
- } catch (Exception ex)
- {
- }
- }
- }};
+ @Override
+ public void run()
+ {
+ SequenceI[] cut = sg.getSequences()
+ .toArray(new SequenceI[sg.getSize()]);
+
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.getAlignment()));
+
+ viewport.setSelectionGroup(null);
+ viewport.sendSelection();
+ viewport.getAlignment().deleteGroup(sg);
+
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+ if (viewport.getAlignment().getHeight() < 1)
+ {
+ try
+ {
+ AlignFrame.this.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }};
/*
* If the cut affects all sequences, prompt for confirmation
boolean wholeHeight = sg.getSize() == viewport.getAlignment().getHeight();
boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
+ 1) == viewport.getAlignment().getWidth()) ? true : false;
- if (wholeHeight && wholeWidth)
- {
- JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
- dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
- Object[] options = new Object[] { MessageManager.getString("action.ok"),
- MessageManager.getString("action.cancel") };
- dialog.showDialog(MessageManager.getString("warn.delete_all"),
- MessageManager.getString("label.delete_all"),
- JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
- options, options[0]);
- } else
- {
- okAction.run();
- }
+ if (wholeHeight && wholeWidth)
+ {
+ JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane());
+ dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
+ Object[] options = new Object[] { MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") };
+ dialog.showDialog(MessageManager.getString("warn.delete_all"),
+ MessageManager.getString("label.delete_all"),
+ JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
+ options, options[0]);
+ } else
+ {
+ okAction.run();
+ }
}
/**
@Override
public void gatherViews_actionPerformed(ActionEvent e)
{
- Desktop.instance.gatherViews(this);
+ Desktop.getInstance().gatherViews(this);
}
/**
{
final boolean setVisible = annotationPanelMenuItem.isSelected();
viewport.setShowAnnotation(setVisible);
- this.showAllSeqAnnotations.setEnabled(setVisible);
- this.hideAllSeqAnnotations.setEnabled(setVisible);
- this.showAllAlAnnotations.setEnabled(setVisible);
- this.hideAllAlAnnotations.setEnabled(setVisible);
+ syncAnnotationMenuItems();
alignPanel.updateLayout();
}
+ private void syncAnnotationMenuItems()
+ {
+ final boolean setVisible = annotationPanelMenuItem.isSelected();
+ showAllSeqAnnotations.setEnabled(setVisible);
+ hideAllSeqAnnotations.setEnabled(setVisible);
+ showAllAlAnnotations.setEnabled(setVisible);
+ hideAllAlAnnotations.setEnabled(setVisible);
+ }
+
+
@Override
public void alignmentProperties()
{
}
JInternalFrame frame = new JInternalFrame();
- final OverviewPanel overview = new OverviewPanel(alignPanel);
+
+ // BH 2019.07.26 we allow for an embedded
+ // undecorated overview with defined size
+ frame.setName(Jalview.getAppID("overview"));
+ //
+ Dimension dim = Platform.getDimIfEmbedded(frame, -1, -1);
+ if (dim != null && dim.width == 0)
+ {
+ dim = null; // hidden, not embedded
+ }
+ OverviewPanel overview = new OverviewPanel(alignPanel, dim);
+
frame.setContentPane(overview);
+ if (dim == null)
+ {
+ dim = new Dimension();
+ // was frame.getSize(), but that is 0,0 at this point;
+ }
+ else
+ {
+ // we are imbedding, and so we have an undecorated frame
+ // and we can set the the frame dimensions accordingly.
+ }
+ // allowing for unresizable option using, style="resize:none"
+ boolean resizable = (Platform.getEmbeddedAttribute(frame,
+ "resize") != "none");
Desktop.addInternalFrame(frame, MessageManager
.formatMessage("label.overview_params", new Object[]
- { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
- true, true);
+ { this.getTitle() }), true, dim.width, dim.height, resizable,
+ true);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(
@Override
public void autoCalculate_actionPerformed(ActionEvent e)
{
- viewport.autoCalculateConsensus = autoCalculate.isSelected();
- if (viewport.autoCalculateConsensus)
+ viewport.setAutoCalculateConsensusAndConservation(autoCalculate.isSelected());
+ if (viewport.getAutoCalculateConsensusAndConservation())
{
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
{
if (_s.getLength() < sg.getEndRes())
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString(
"label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
MessageManager.getString(
frameTitle += this.title;
- Desktop.addInternalFrame(tp, frameTitle, 600, 500);
+ Dimension dim = Platform.getDimIfEmbedded(tp, 600, 500);
+ Desktop.addInternalFrame(tp, frameTitle, dim.width, dim.height);
}
/**
viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
} catch (Exception ex)
{
- JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), ex.getMessage(),
MessageManager
.getString("label.problem_reading_tree_file"),
JvOptionPane.WARNING_MESSAGE);
}
if (fin != null && fin.hasWarningMessage())
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
fin.getWarningMessage(),
MessageManager.getString(
"label.possible_problem_with_tree_file"),
if (nf.getTree() != null)
{
tp = new TreePanel(alignPanel, nf, treeTitle, input);
-
- tp.setSize(w, h);
+ Dimension dim = Platform.getDimIfEmbedded(tp, -1, -1);
+ if (dim == null)
+ {
+ dim = new Dimension(w, h);
+ }
+ else
+ {
+ // no offset, either
+ x = 0;
+ }
+ tp.setSize(dim.width, dim.height);
if (x > 0 && y > 0)
{
tp.setLocation(x, y);
}
- Desktop.addInternalFrame(tp, treeTitle, w, h);
+ Desktop.addInternalFrame(tp, treeTitle, dim.width, dim.height);
}
} catch (Exception ex)
{
*/
public void BuildWebServiceMenu()
{
+ if (Jalview.isSynchronous())
+ {
+ return;
+ }
while (buildingMenu)
{
try
final JMenu dismenu = new JMenu("Protein Disorder");
// JAL-940 - only show secondary structure prediction services from
// the legacy server
+ Hashtable<String, Vector<ServiceHandle>> services = Discoverer
+ .getInstance().getServices();
if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
- // &&
- Discoverer.services != null && (Discoverer.services.size() > 0))
+ // &&
+ services != null && (services.size() > 0))
{
// TODO: refactor to allow list of AbstractName/Handler bindings to
// be
// No MSAWS used any more:
// Vector msaws = null; // (Vector)
// Discoverer.services.get("MsaWS");
- Vector<ServiceHandle> secstrpr = Discoverer.services
- .get("SecStrPred");
+ Vector<ServiceHandle> secstrpr = services.get("SecStrPred");
if (secstrpr != null)
{
// Add any secondary structure prediction services
webService.add(me.webServiceNoServices);
}
// TODO: move into separate menu builder class.
- boolean new_sspred = false;
+ // boolean new_sspred = false;
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
+ Jws2Discoverer jws2servs = Jws2Discoverer.getInstance();
if (jws2servs != null)
{
if (jws2servs.hasServices())
final String errorTitle = MessageManager
.getString("label.implementation_error")
+ MessageManager.getString("label.translation_failed");
- JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, errorTitle,
JvOptionPane.ERROR_MESSAGE);
return;
}
"label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
final String errorTitle = MessageManager
.getString("label.translation_failed");
- JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, errorTitle,
JvOptionPane.WARNING_MESSAGE);
}
else
if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
- viewport.openSplitFrame(af, new Alignment(seqs));
+ AlignViewport.openSplitFrame(this, af, new Alignment(seqs));
}
else
{
{
// BH 2018
return avc.parseFeaturesFile(file, sourceType,
- Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+ Cache.getDefault(Preferences.RELAXEDSEQIDMATCHING, false));
}
if (filesmatched.size() > 0)
{
boolean autoAssociate = Cache
- .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
+ .getDefault(Preferences.AUTOASSOCIATE_PDBANDSEQS, false);
if (!autoAssociate)
{
String msg = MessageManager.formatMessage(
// associating PDB files which have no IDs.
for (SequenceI toassoc : (SequenceI[]) fm[2])
{
- PDBEntry pe = new AssociatePdbFileWithSeq()
+ // BH! check
+ PDBEntry pe = AssociatePdbFileWithSeq
.associatePdbWithSeq(fm[0].toString(),
- (DataSourceType) fm[1], toassoc, false,
- Desktop.instance);
+ (DataSourceType) fm[1], toassoc, false);
if (pe != null)
{
System.err.println("Associated file : "
{
// some problem - if no warning its probable that the ID matching
// process didn't work
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
tcf.getWarningMessage() == null
? MessageManager.getString(
"label.check_file_matches_sequence_ids_alignment")
}
else
{
- alignPanel.paintAlignment(true, true);
- }
+ alignPanel.paintAlignment(true, true);
}
}
+ }
else
{
- new FileLoader().LoadFile(viewport, file, sourceType, format);
+ if (file instanceof File) {
+ new FileLoader().loadFile(viewport, (File) file, sourceType, format);
+ } else {
+ new FileLoader().LoadFile(viewport, (String) file, sourceType, format);
+ }
}
}
}
if (isAnnotation)
{
-
- alignPanel.adjustAnnotationHeight();
- viewport.updateSequenceIdColours();
- buildSortByAnnotationScoresMenu();
- alignPanel.paintAlignment(true, true);
+ updateForAnnotations();
}
} catch (Exception ex)
{
+ (format != null
? "(parsing as '" + format + "' file)"
: ""),
- oom, Desktop.desktop);
+ oom, Desktop.getDesktopPane());
}
}
/**
+ * Do all updates necessary after an annotation file such as jnet. Also called
+ * from Jalview.loadAppletParams for "annotations", "jnetFile"
+ */
+ public void updateForAnnotations()
+ {
+ alignPanel.adjustAnnotationHeight();
+ viewport.updateSequenceIdColours();
+ buildSortByAnnotationScoresMenu();
+ alignPanel.paintAlignment(true, true);
+ }
+
+ /**
* Method invoked by the ChangeListener on the tabbed pane, in other words
* when a different tabbed pane is selected by the user or programmatically.
*/
{
// refresh the featureSettings to reflect UI change
showFeatureSettingsUI();
- }
+ }
else
{
// close feature settings for this view.
}
/**
+ * Change the display state for the given feature groups -- Added by BH from
+ * JalviewLite
+ *
+ * @param groups
+ * list of group strings
+ * @param state
+ * visible or invisible
+ */
+ public void setFeatureGroupState(String[] groups, boolean state)
+ {
+ jalview.api.FeatureRenderer fr = null;
+ viewport.setShowSequenceFeatures(true);
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
+ {
+
+ fr.setGroupVisibility(Arrays.asList(groups), state);
+ alignPanel.getSeqPanel().seqCanvas.repaint();
+ if (alignPanel.overviewPanel != null)
+ {
+ alignPanel.overviewPanel.updateOverviewImage();
+ }
+ }
+ }
+
+ /**
* Open the dialog for regex description parsing.
*/
@Override
});
rfetch.add(fetchr);
- new Thread(new Runnable()
+ Jalview.execThread(new Thread(new Runnable()
{
@Override
public void run()
{
- final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
- .getSequenceFetcherSingleton();
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ Jalview.execRunnable(new Runnable()
{
@Override
public void run()
{
- String[] dbclasses = sf.getNonAlignmentSources();
+ String[] dbclasses = jalview.ws.SequenceFetcher.getInstance()
+ .getNonAlignmentSources();
List<DbSourceProxy> otherdb;
JMenu dfetch = new JMenu();
JMenu ifetch = new JMenu();
int dbi = 0;
for (String dbclass : dbclasses)
{
- otherdb = sf.getSourceProxy(dbclass);
+ otherdb = jalview.ws.SequenceFetcher.getInstance()
+ .getSourceProxy(dbclass);
// add a single entry for this class, or submenu allowing 'fetch
// all' or pick one
if (otherdb == null || otherdb.size() < 1)
}
if (otherdb.size() == 1)
{
- final DbSourceProxy[] dassource = otherdb
- .toArray(new DbSourceProxy[0]);
+ // BH cleaner code
DbSourceProxy src = otherdb.get(0);
+ DbSourceProxy[] dassource = new DbSourceProxy[] {
+ src };
fetchr = new JMenuItem(src.getDbSource());
fetchr.addActionListener(new ActionListener()
{
}
});
}
- }).start();
+ }));
}
} catch (Exception ex)
{
System.err.println((ex.toString()));
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.couldnt_run_groovy_script"),
MessageManager.getString("label.groovy_support_failed"),
JvOptionPane.ERROR_MESSAGE);
}
+
private Rectangle lastFeatureSettingsBounds = null;
@Override
public void setFeatureSettingsGeometry(Rectangle bounds)
{
return lastFeatureSettingsBounds;
}
+
+ /**
+ * BH 2019 from JalviewLite
+ *
+ * get sequence feature groups that are hidden or shown
+ *
+ * @param visible
+ * true is visible
+ * @return list
+ */
+ public String[] getFeatureGroupsOfState(boolean visible)
+ {
+ jalview.api.FeatureRenderer fr = null;
+ if (alignPanel != null
+ && (fr = alignPanel
+ .getFeatureRenderer()) != null)
+ {
+ List<String> gps = fr.getGroups(visible);
+ String[] _gps = gps.toArray(new String[gps.size()]);
+ return _gps;
+ }
+ return null;
+ }
+
+ public void scrollTo(int row, int column)
+ {
+ alignPanel.getSeqPanel().scrollTo(row, column);
+ }
+
+ public void scrollToRow(int row)
+ {
+ alignPanel.getSeqPanel().scrollToRow(row);
+ }
+
+ public void scrollToColumn(int column)
+ {
+ alignPanel.getSeqPanel().scrollToColumn(column);
+ }
+
+ /**
+ *
+ * @return list of feature groups on the view
+ */
+ public String[] getFeatureGroups()
+ {
+ jalview.api.FeatureRenderer fr = null;
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
+ {
+ List<String> gps = fr.getFeatureGroups();
+ String[] _gps = gps.toArray(new String[gps.size()]);
+ return _gps;
+ }
+ return null;
+ }
+
+ public void select(SequenceGroup sel, ColumnSelection csel,
+ HiddenColumns hidden)
+ {
+ alignPanel.getSeqPanel().selection(sel, csel, hidden, null);
+ }
+
}
class PrintThread extends Thread
}
}
}
+
}
*/
private void applyViewProperties()
{
- antiAlias = Cache.getDefault("ANTI_ALIAS", true);
-
- viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
- setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
-
- setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
- setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
- autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
-
- setPadGaps(Cache.getDefault("PAD_GAPS", true));
- setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
- setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
- viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
- viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
+ // BH! using final static strings here because we also use these in
+ // JS version startup api
+ // BH was false
+ antiAlias = Cache.getDefault(Preferences.ANTI_ALIAS, true);
+
+ viewStyle.setShowJVSuffix(
+ Cache.getDefault(Preferences.SHOW_JVSUFFIX, true));
+ setShowAnnotation(Cache.getDefault(Preferences.SHOW_ANNOTATIONS, true));
+
+ setRightAlignIds(Cache.getDefault(Preferences.RIGHT_ALIGN_IDS, false));
+ setCentreColumnLabels(Cache.getDefault(Preferences.CENTRE_COLUMN_LABELS, false));
+ autoCalculateConsensusAndConservation = Cache.getDefault(Preferences.AUTO_CALC_CONSENSUS, true);
+
+ setPadGaps(Cache.getDefault(Preferences.PAD_GAPS, true));
+ setShowNPFeats(Cache.getDefault(Preferences.SHOW_NPFEATS_TOOLTIP, true));
+ setShowDBRefs(Cache.getDefault(Preferences.SHOW_DBREFS_TOOLTIP, true));
+ viewStyle.setSeqNameItalics(Cache.getDefault(Preferences.ID_ITALICS, true));
+ viewStyle.setWrapAlignment(
+ Cache.getDefault(Preferences.WRAP_ALIGNMENT, false));
viewStyle.setShowUnconserved(
- Cache.getDefault("SHOW_UNCONSERVED", false));
- sortByTree = Cache.getDefault("SORT_BY_TREE", false);
- followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
+ Cache.getDefault(Preferences.SHOW_UNCONSERVED, false));
+ sortByTree = Cache.getDefault(Preferences.SORT_BY_TREE, false);
+ followSelection = Cache.getDefault(Preferences.FOLLOW_SELECTIONS, true);
sortAnnotationsBy = SequenceAnnotationOrder
.valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
SequenceAnnotationOrder.NONE.name()));
{
applyViewProperties();
- String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
- String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
- String fontSize = Cache.getDefault("FONT_SIZE", "10");
+ String fontName = Cache.getDefault(Preferences.FONT_NAME, "SansSerif");
+ String fontStyle = Cache.getDefault(Preferences.FONT_STYLE,
+ Font.PLAIN + "");
+ String fontSize = Cache.getDefault(Preferences.FONT_SIZE, "10");
int style = 0;
setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
alignment
- .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+ .setGapCharacter(Cache.getDefault(Preferences.GAP_SYMBOL, "-")
+ .charAt(0));
// We must set conservation and consensus before setting colour,
// as Blosum and Clustal require this to be done
{
if (!alignment.isNucleotide())
{
- showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
- showQuality = Cache.getDefault("SHOW_QUALITY", true);
- showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
- false);
+ showConservation = Cache.getDefault(Preferences.SHOW_CONSERVATION,
+ true);
+ showQuality = Cache.getDefault(Preferences.SHOW_QUALITY, true);
+ showGroupConservation = Cache
+ .getDefault(Preferences.SHOW_GROUP_CONSERVATION, false);
}
- showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
- true);
- showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
- normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
+ showConsensusHistogram = Cache
+ .getDefault(Preferences.SHOW_CONSENSUS_HISTOGRAM, true);
+ showSequenceLogo = Cache.getDefault(Preferences.SHOW_CONSENSUS_LOGO,
false);
- showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
- showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
+
+ normaliseSequenceLogo = Cache
+ .getDefault(Preferences.NORMALISE_CONSENSUS_LOGO, false);
+ showGroupConsensus = Cache
+ .getDefault(Preferences.SHOW_GROUP_CONSENSUS, false);
+ showConsensus = Cache.getDefault(Preferences.SHOW_IDENTITY, true);
showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
}
*/
if (align != null)
{
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- ssm.registerMappings(align.getCodonFrames());
+ Desktop.getStructureSelectionManager()
+ .registerMappings(align.getCodonFrames());
}
/*
List<AlignedCodonFrame> mappings = al.getCodonFrames();
if (mappings != null)
{
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ StructureSelectionManager ssm = Desktop
+ .getStructureSelectionManager();
for (AlignedCodonFrame acf : mappings)
{
if (noReferencesTo(acf))
@Override
public void sendSelection()
{
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
- .sendSelection(new SequenceGroup(getSelectionGroup()),
- new ColumnSelection(getColumnSelection()),
- new HiddenColumns(getAlignment().getHiddenColumns()),
- this);
+ Desktop.getStructureSelectionManager().sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()),
+ new HiddenColumns(getAlignment().getHiddenColumns()), this);
}
/**
@Override
public StructureSelectionManager getStructureSelectionManager()
{
- return StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ return Desktop.getStructureSelectionManager();
}
@Override
firePropertyChange("alignment", null, getAlignment().getSequences());
}
+ public final static int NO_SPLIT = 0;
+
+ public final static int SPLIT_FRAME = 1;
+
+ public final static int NEW_WINDOW = 2;
+
/**
* Show a dialog with the option to open and link (cDNA <-> protein) as a new
* alignment, either as a standalone alignment or in a split frame. Returns
MessageManager.getString("label.new_window"), };
final String question = JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.open_split_window?"));
- final AlignViewport us = this;
-
+
/*
* options No, Split Window, New Window correspond to
* dialog responses 0, 1, 2 (even though JOptionPane shows them
* in reverse order)
*/
- JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
- .setResponseHandler(0, new Runnable()
+ JvOptionPane dialog = JvOptionPane
+ .newOptionDialog(Desktop.getDesktopPane())
+ .setResponseHandler(NO_SPLIT, new Runnable()
{
@Override
public void run()
{
- addDataToAlignment(al);
+ addDataToAlignment(al);
}
- }).setResponseHandler(1, new Runnable()
+ }).setResponseHandler(SPLIT_FRAME, new Runnable()
{
@Override
public void run()
{
- us.openLinkedAlignmentAs(al, title, true);
+ openLinkedAlignmentAs(getAlignPanel().alignFrame,
+ new Alignment(getAlignment()), al, title,
+ SPLIT_FRAME);
}
- }).setResponseHandler(2, new Runnable()
+ }).setResponseHandler(NEW_WINDOW, new Runnable()
{
@Override
public void run()
{
- us.openLinkedAlignmentAs(al, title, false);
+ openLinkedAlignmentAs(null, getAlignment(), al, title,
+ NEW_WINDOW);
}
});
- dialog.showDialog(question,
+ dialog.showDialog(question,
MessageManager.getString("label.open_split_window"),
JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
options, options[0]);
}
- protected void openLinkedAlignmentAs(AlignmentI al, String title,
- boolean newWindowOrSplitPane)
- {
- /*
- * Identify protein and dna alignments. Make a copy of this one if opening
- * in a new split pane.
- */
- AlignmentI thisAlignment = newWindowOrSplitPane
- ? new Alignment(getAlignment())
- : getAlignment();
+ /**
+ * Open a split frame or a new window
+ *
+ * @param al
+ * @param title
+ * @param mode
+ * SPLIT_FRAME or NEW_WINDOW
+ */
+ public static void openLinkedAlignmentAs(AlignFrame thisFrame,
+ AlignmentI thisAlignment, AlignmentI al, String title, int mode)
+ {
+ // BH: thisAlignment is already a copy if mode == SPLIT_FRAME
+ // Identify protein and dna alignments. Make a copy of this one if opening
+ // in a new split pane.
+
AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
- final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
+ AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
/*
* Map sequences. At least one should get mapped as we have already passed
// alignFrame.setFileName(file, format);
// }
- if (!newWindowOrSplitPane)
+ if (mode == NEW_WINDOW)
{
Desktop.addInternalFrame(newAlignFrame, title,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
try
{
- newAlignFrame.setMaximum(
- jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+ newAlignFrame.setMaximum(Cache.getDefault(Preferences.SHOW_FULLSCREEN, false));
} catch (java.beans.PropertyVetoException ex)
{
}
- if (newWindowOrSplitPane)
+ if (mode == SPLIT_FRAME)
{
al.alignAs(thisAlignment);
- protein = openSplitFrame(newAlignFrame, thisAlignment);
+ openSplitFrame(thisFrame, newAlignFrame, thisAlignment);
}
}
* cdna/protein complement alignment to show in the other split half
* @return the protein alignment in the split frame
*/
- protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
- AlignmentI complement)
+ static protected AlignmentI openSplitFrame(AlignFrame thisFrame,
+ AlignFrame newAlignFrame, AlignmentI complement)
{
/*
* Make a new frame with a copy of the alignment we are adding to. If this
*/
AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
+ copyMe.setTitle(thisFrame.getTitle());
AlignmentI al = newAlignFrame.viewport.getAlignment();
final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
{
return;
}
-
+
FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
.getFeatureRenderer();
- List<String> origRenderOrder = new ArrayList(),
- origGroups = new ArrayList();
+ List<String> origRenderOrder = new ArrayList<>(),
+ origGroups = new ArrayList<>();
// preserve original render order - allows differentiation between user configured colours and autogenerated ones
origRenderOrder.addAll(fr.getRenderOrder());
origGroups.addAll(fr.getFeatureGroups());
FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
if (!mergeOnly)
{
- // only clear displayed features if we are mergeing
- displayed.clear();
+ // only clear displayed features if we are merging
+ displayed.clear();
}
// TODO this clears displayed.featuresRegistered - do we care?
//
{
// if we are merging, only update if there wasn't already a colour defined for
// this type
- if (preferredColour != null)
- {
- fr.setColour(type, preferredColour);
- }
- if (featureSettings.isFeatureDisplayed(type))
- {
- displayed.setVisible(type);
- }
+ if (preferredColour != null)
+ {
+ fr.setColour(type, preferredColour);
}
+ if (featureSettings.isFeatureDisplayed(type))
+ {
+ displayed.setVisible(type);
+ }
+ }
}
/*
updateView();
}
};
- JalviewColourChooser.showColourChooser(Desktop.getDesktop(), ttl,
+ JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(), ttl,
colourPanel.getBackground(), listener);
}
seqs, omitHidden, alignmentStartEnd);
Toolkit.getDefaultToolkit().getSystemClipboard()
- .setContents(new StringSelection(output), Desktop.instance);
+ .setContents(new StringSelection(output), Desktop.getInstance());
HiddenColumns hiddenColumns = null;
}
if (errormsgs.length() > 0)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.pdb_entries_couldnt_be_retrieved", new String[]
{ errormsgs.toString() }),
*/
package jalview.gui;
-import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
-import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
-import javax.swing.JOptionPane;
-
/**
- * GUI related routines for associating PDB files with sequences
+ * GUI related routines for associating PDB files with sequences. A single
+ * static method.
*
* @author JimP
*
public class AssociatePdbFileWithSeq
{
+ private AssociatePdbFileWithSeq()
+ {
+ // inaccessible
+ }
+
/**
- * assocate the given PDB file with
+ * Associate the given PDB file name or URL with a sequence. Do not map
+ * mouse-over events.
*
- * @param choice
+ * @param fileName
+ * or URL
+ * @param type
+ * will be DataType.FILE or DataType.URL
* @param sequence
+ * to associate
+ * @param prompt
+ * true if the user should be asked what to do if the specified file
+ * does not seem to contain PDB information (StructureChooser only)
+ * @return null if file is not found
*/
- public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
- SequenceI sequence, boolean prompt,
- StructureSelectionManagerProvider ssmp)
+ public static PDBEntry associatePdbWithSeq(String fileName,
+ DataSourceType type, SequenceI sequence, boolean prompt)
{
PDBEntry entry = new PDBEntry();
StructureFile pdbfile = null;
- pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
+ pdbfile = Desktop.getStructureSelectionManager()
.setMapping(false, new SequenceI[]
- { sequence }, null, choice, file);
+ { sequence }, null, fileName, type);
if (pdbfile == null)
{
// stacktrace already thrown so just return
return null;
}
- if (pdbfile.getId() == null)
- {
- String reply = null;
-
- if (prompt)
- {
- reply = JvOptionPane.showInternalInputDialog(Desktop.desktop,
- MessageManager
- .getString("label.couldnt_find_pdb_id_in_file"),
- MessageManager.getString("label.no_pdb_id_in_file"),
- JvOptionPane.QUESTION_MESSAGE);
- }
- if (reply == null)
- {
- return null;
- }
-
- entry.setId(reply);
- }
- else
+ String id = pdbfile.getId();
+ if (id == null && (id = (prompt
+ ? JvOptionPane.showInternalInputDialog(Desktop.getDesktopPane(),
+ MessageManager
+ .getString("label.couldnt_find_pdb_id_in_file"),
+ MessageManager.getString("label.no_pdb_id_in_file"),
+ JvOptionPane.QUESTION_MESSAGE)
+ : null)) == null)
{
- entry.setId(pdbfile.getId());
+ return null;
}
+ entry.setId(id);
entry.setType(PDBEntry.Type.FILE);
-
- if (pdbfile != null)
- {
- entry.setFile(choice);
- sequence.getDatasetSequence().addPDBId(entry);
- StructureSelectionManager.getStructureSelectionManager(ssmp)
- .registerPDBEntry(entry);
- }
+ entry.setFile(fileName);
+ sequence.getDatasetSequence().addPDBId(entry);
+ Desktop.getInstance().getStructureSelectionManager()
+ .registerPDBEntry(entry);
return entry;
}
}
import javax.swing.event.InternalFrameEvent;
/**
- * A dialog where a user can choose and action Tree or PCA calculation options
+ * A dialog where a user can choose and action Tree or PCA calculation options.
+ *
+ * Allows also for dialog-free static methods openPCAPanel(...) and
+ * openTreePanel(...) for scripted use.
+ *
*/
+@SuppressWarnings("serial")
public class CalculationChooser extends JPanel
{
/*
*/
private static boolean treeMatchGaps = true;
- private static final Font VERDANA_11PT = new Font("Verdana", 0, 11);
+ private static Font VERDANA_11PT;
private static final int MIN_TREE_SELECTION = 3;
private JCheckBox shorterSequence;
- final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
+ private static ComboBoxTooltipRenderer renderer; // BH was not static
List<String> tips = new ArrayList<>();
private PCAPanel pcaPanel;
/**
+ * Open a new Tree panel on the desktop statically. Params are standard (not
+ * set by Groovy). No dialog is opened.
+ *
+ * @param af
+ * @param treeType
+ * @param modelName
+ * @return null if successful; the string
+ * "label.you_need_at_least_n_sequences" if number of sequences
+ * selected is inappropriate
+ */
+ public static Object openTreePanel(AlignFrame af, String treeType,
+ String modelName)
+ {
+ return openTreePanel(af, treeType, modelName, null);
+ }
+
+ /**
+ * public static method for JalviewJS API to open a PCAPanel without
+ * necessarily using a dialog.
+ *
+ * @param af
+ * @param modelName
+ * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
+ * if number of sequences selected is inappropriate
+ */
+ public static Object openPcaPanel(AlignFrame af, String modelName)
+ {
+ return openPcaPanel(af, modelName, null);
+ }
+
+ /**
* Constructor
*
* @param af
paramsPanel.add(includeGappedColumns);
paramsPanel.add(shorterSequence);
+ if (VERDANA_11PT == null)
+ {
+ VERDANA_11PT = new Font("Verdana", 0, 11);
+ }
/*
* OK / Cancel buttons
*/
*/
protected JComboBox<String> buildModelOptionsList()
{
- final JComboBox<String> scoreModelsCombo = new JComboBox<>();
+ JComboBox<String> scoreModelsCombo = new JComboBox<>();
+ if (renderer == null)
+ {
+ renderer = new ComboBoxTooltipRenderer();
+ }
scoreModelsCombo.setRenderer(renderer);
/*
* for backwards compatibility with Jalview < 2.8 (JAL-2962)
*/
if (nucleotide && forPca
- && Cache.getDefault("BLOSUM62_PCA_FOR_NUCLEOTIDE", false))
+ && Cache.getDefault(Preferences.BLOSUM62_PCA_FOR_NUCLEOTIDE,
+ false))
{
filtered.add(scoreModels.getBlosum62());
}
*/
protected void openTreePanel(String modelName, SimilarityParamsI params)
{
+ Object ret = openTreePanel(af,
+ neighbourJoining.isSelected() ? TreeBuilder.NEIGHBOUR_JOINING
+ : TreeBuilder.AVERAGE_DISTANCE,
+ modelName, params);
+ if (ret instanceof String)
+ {
+ JvOptionPane.showMessageDialog(this, // was opening on Desktop?
+ MessageManager.formatMessage(
+ (String) ret,
+ MIN_TREE_SELECTION),
+ MessageManager.getString("label.not_enough_sequences"),
+ JvOptionPane.WARNING_MESSAGE);
+
+ }
+ }
+
+ /**
+ * Open a new PCA panel on the desktop
+ *
+ * @param modelName
+ * @param params
+ */
+ protected void openPcaPanel(String modelName, SimilarityParamsI params)
+ {
+ Object ret = openPcaPanel(af, modelName, params);
+ if (ret instanceof String)
+ {
+ JvOptionPane.showInternalMessageDialog(this,
+ MessageManager.formatMessage(
+ (String) ret,
+ MIN_PCA_SELECTION),
+ MessageManager
+ .getString("label.sequence_selection_insufficient"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
+ // only used for test suite
+ pcaPanel = (PCAPanel) ret;
+ }
+
+ }
+
+ /**
+ * Open a new Tree panel on the desktop statically
+ *
+ * @param af
+ * @param treeType
+ * @param modelName
+ * @param params
+ * @return null, or the string "label.you_need_at_least_n_sequences" if number
+ * of sequences selected is inappropriate
+ */
+ public static Object openTreePanel(AlignFrame af, String treeType,
+ String modelName, SimilarityParamsI params)
+ {
+
/*
* gui validation shouldn't allow insufficient sequences here, but leave
* this check in in case this method gets exposed programmatically in future
SequenceGroup sg = viewport.getSelectionGroup();
if (sg != null && sg.getSize() < MIN_TREE_SELECTION)
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.you_need_at_least_n_sequences",
- MIN_TREE_SELECTION),
- MessageManager.getString("label.not_enough_sequences"),
- JvOptionPane.WARNING_MESSAGE);
- return;
+ return "label.you_need_at_least_n_sequences";
+ }
+
+ if (params == null)
+ {
+ params = getSimilarityParameters(false);
}
- String treeType = neighbourJoining.isSelected()
- ? TreeBuilder.NEIGHBOUR_JOINING
- : TreeBuilder.AVERAGE_DISTANCE;
af.newTreePanel(treeType, modelName, params);
+ return null;
}
/**
- * Open a new PCA panel on the desktop
+ * public static method for JalviewJS API
*
+ * @param af
* @param modelName
* @param params
+ * @return the PCAPanel, or null if number of sequences selected is
+ * inappropriate
*/
- protected void openPcaPanel(String modelName, SimilarityParamsI params)
+ public static Object openPcaPanel(AlignFrame af, String modelName,
+ SimilarityParamsI params)
{
+
AlignViewport viewport = af.getViewport();
/*
* gui validation shouldn't allow insufficient sequences here, but leave
* this check in in case this method gets exposed programmatically in future
+ *
+ *
*/
if (((viewport.getSelectionGroup() != null)
&& (viewport.getSelectionGroup().getSize() < MIN_PCA_SELECTION)
&& (viewport.getSelectionGroup().getSize() > 0))
|| (viewport.getAlignment().getHeight() < MIN_PCA_SELECTION))
{
- JvOptionPane.showInternalMessageDialog(this,
- MessageManager.formatMessage(
- "label.you_need_at_least_n_sequences",
- MIN_PCA_SELECTION),
- MessageManager
- .getString("label.sequence_selection_insufficient"),
- JvOptionPane.WARNING_MESSAGE);
- return;
+ return "label.you_need_at_least_n_sequences";
+ }
+
+ if (params == null)
+ {
+ params = getSimilarityParameters(true);
}
/*
* construct the panel and kick off its calculation thread
*/
- pcaPanel = new PCAPanel(af.alignPanel, modelName, params);
- new Thread(pcaPanel).start();
-
+ PCAPanel pcap = new PCAPanel(af.alignPanel, modelName, params);
+ new Thread(pcap).start();
+ return pcap;
}
/**
}
}
+
/**
* Returns a data bean holding parameters for similarity (or distance) model
* calculation
* @param doPCA
* @return
*/
- protected SimilarityParamsI getSimilarityParameters(boolean doPCA)
+ public static SimilarityParamsI getSimilarityParameters(
+ boolean doPCA)
{
// commented out: parameter choices read from gui widgets
// SimilarityParamsI params = new SimilarityParams(
return new SimilarityParams(includeGapGap, matchGap, includeGapResidue,
matchOnShortestLength);
+
}
/**
if (!jmb.launchChimera())
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.chimera_failed"),
MessageManager.getString("label.error_loading_file"),
JvOptionPane.ERROR_MESSAGE);
if (errormsgs.length() > 0)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.pdb_entries_couldnt_be_retrieved", new Object[]
{ errormsgs.toString() }),
ActionListener al = radioItem.getActionListeners()[0];
radioItem.removeActionListener(al);
int option = JvOptionPane.showInternalConfirmDialog(
- Desktop.desktop,
+ Desktop.getDesktopPane(),
MessageManager
.getString("label.remove_from_default_list"),
MessageManager
}
else
{
- Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
+ Cache.removePropertyNoSave("USER_DEFINED_COLOURS");
}
}
}
.setGapCharacter(alignFrame.viewport.getGapCharacter());
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
/*
* register any new mappings for sequence mouseover etc
.println(MessageManager.getString("label.couldnt_read_data"));
if (!Jalview.isHeadlessMode())
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
AppletFormatAdapter.getSupportedFormats(),
MessageManager.getString("label.couldnt_read_data"),
JvOptionPane.WARNING_MESSAGE);
} catch (IOException ex)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager
.formatMessage("label.couldnt_read_pasted_text", new String[]
{ ex.toString() }),
MessageManager.getString("label.error_parsing_text"),
.println(MessageManager.getString("label.couldnt_read_data"));
if (!Jalview.isHeadlessMode())
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
AppletFormatAdapter.getSupportedFormats(),
MessageManager.getString("label.couldnt_read_data"),
JvOptionPane.WARNING_MESSAGE);
import java.beans.PropertyChangeListener;
import java.io.File;
import java.io.FileWriter;
+
import java.io.IOException;
+import java.lang.reflect.Method;
import java.net.URL;
import java.util.ArrayList;
import java.util.HashMap;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+import java.io.BufferedInputStream;
+import java.io.FileOutputStream;
+import javax.swing.JFrame;
+import jalview.api.StructureSelectionManagerProvider;
+
import org.stackoverflowusers.file.WindowsShortcut;
import jalview.api.AlignViewportI;
*/
public class Desktop extends jalview.jbgui.GDesktop
implements DropTargetListener, ClipboardOwner, IProgressIndicator,
- jalview.api.StructureSelectionManagerProvider
+ StructureSelectionManagerProvider, ApplicationSingletonI
{
private static final String CITATION = "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
+ "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
private static final String DEFAULT_AUTHORS = "The Jalview Authors (See AUTHORS file for current list)";
- private static int DEFAULT_MIN_WIDTH = 300;
+ private final static int DEFAULT_MIN_WIDTH = 300;
- private static int DEFAULT_MIN_HEIGHT = 250;
+ private final static int DEFAULT_MIN_HEIGHT = 250;
- private static int ALIGN_FRAME_DEFAULT_MIN_WIDTH = 600;
+ private final static int ALIGN_FRAME_DEFAULT_MIN_WIDTH = 600;
- private static int ALIGN_FRAME_DEFAULT_MIN_HEIGHT = 70;
+ private final static int ALIGN_FRAME_DEFAULT_MIN_HEIGHT = 70;
- private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
+ private final static String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
protected static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT";
listener);
}
- /** Singleton Desktop instance */
- public static Desktop instance;
-
- public static MyDesktopPane desktop;
-
- public static MyDesktopPane getDesktop()
+ public static StructureSelectionManager getStructureSelectionManager()
{
- // BH 2018 could use currentThread() here as a reference to a
- // Hashtable<Thread, MyDesktopPane> in JavaScript
- return desktop;
+ return StructureSelectionManager
+ .getStructureSelectionManager(getInstance());
}
static int openFrameCount = 0;
static final int yOffset = 30;
- public static jalview.ws.jws1.Discoverer discoverer;
+ // BH was static
+ public jalview.ws.jws1.Discoverer discoverer;
+
+ //BH was static
+ public Object[] jalviewClipboard;
+
+//BH was static
+ public boolean internalCopy = false;
- public static Object[] jalviewClipboard;
+ private static int fileLoadingCount = 0;
- public static boolean internalCopy = false;
+ public JInternalFrame conservationSlider;
- static int fileLoadingCount = 0;
+ public JInternalFrame PIDSlider;
class MyDesktopManager implements DesktopManager
{
} catch (NullPointerException npe)
{
Point p = getMousePosition();
- instance.showPasteMenu(p.x, p.y);
+ showPasteMenu(p.x, p.y);
}
}
public void endDraggingFrame(JComponent f)
{
delegate.endDraggingFrame(f);
- desktop.repaint();
+ desktopPane.repaint();
}
@Override
public void endResizingFrame(JComponent f)
{
delegate.endResizingFrame(f);
- desktop.repaint();
+ desktopPane.repaint();
}
@Override
// All other methods, simply delegate
}
-
/**
- * Creates a new Desktop object.
+ * Private constructor enforces singleton pattern. It is called by reflection
+ * from ApplicationSingletonProvider.getInstance().
*/
- public Desktop()
+ private Desktop()
{
- super();
- /**
- * A note to implementors. It is ESSENTIAL that any activities that might
- * block are spawned off as threads rather than waited for during this
- * constructor.
- */
- instance = this;
-
- doConfigureStructurePrefs();
- setTitle("Jalview " + Cache.getProperty("VERSION"));
- /*
- if (!Platform.isAMac())
- {
- // this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
- }
- else
- {
- this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
- }
- */
-
+ Cache.initLogger();
try
{
- APQHandlers.setAPQHandlers(this);
- } catch (Throwable t)
- {
- System.out.println("Error setting APQHandlers: " + t.toString());
- // t.printStackTrace();
- }
-
- addWindowListener(new WindowAdapter()
- {
+ /**
+ * A note to implementors. It is ESSENTIAL that any activities that might
+ * block are spawned off as threads rather than waited for during this
+ * constructor.
+ */
- @Override
- public void windowClosing(WindowEvent ev)
+ doConfigureStructurePrefs();
+ setTitle("Jalview " + Cache.getProperty("VERSION"));
+
+ try
{
- quit();
+ if (Platform.getJavaVersion() >= 11)
+ {
+ // BH use reflection so that this code can be in both the Java8 and Java11 versions
+ Class<?> j11APQHandlers = Class.forName("jalview.gui.APQHandlers");
+ Method meth = j11APQHandlers.getMethod("setAPQHandlers", new Class<?>[] {Desktop.class});
+ meth.invoke(j11APQHandlers.newInstance(), this);
+ }
+ } catch (Throwable t)
+ {
+ System.out.println("Desktop Error setting APQHandlers: " + t.toString());
}
- });
- boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE",
- false);
+ addWindowListener(new WindowAdapter()
+ {
+
+ @Override
+ public void windowClosing(WindowEvent ev)
+ {
+ quit();
+ }
+ });
+
+ boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE",
+ false);
boolean showjconsole = Cache.getDefault("SHOW_JAVA_CONSOLE",
false);
- desktop = new MyDesktopPane(selmemusage);
+ desktopPane = new MyDesktopPane(selmemusage);
showMemusage.setSelected(selmemusage);
- desktop.setBackground(Color.white);
+ desktopPane.setBackground(Color.white);
- getContentPane().setLayout(new BorderLayout());
- // alternate config - have scrollbars - see notes in JAL-153
- // JScrollPane sp = new JScrollPane();
- // sp.getViewport().setView(desktop);
- // getContentPane().add(sp, BorderLayout.CENTER);
+ getContentPane().setLayout(new BorderLayout());
+ // alternate config - have scrollbars - see notes in JAL-153
+ // JScrollPane sp = new JScrollPane();
+ // sp.getViewport().setView(desktop);
+ // getContentPane().add(sp, BorderLayout.CENTER);
- // BH 2018 - just an experiment to try unclipped JInternalFrames.
- if (Platform.isJS())
- {
- getRootPane().putClientProperty("swingjs.overflow.hidden", "false");
- }
+ // BH 2018 - just an experiment to try unclipped JInternalFrames.
+ if (Platform.isJS())
+ {
+ getRootPane().putClientProperty("swingjs.overflow.hidden", "false");
+ }
- getContentPane().add(desktop, BorderLayout.CENTER);
- desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
+ getContentPane().add(desktopPane, BorderLayout.CENTER);
+ desktopPane.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
- // This line prevents Windows Look&Feel resizing all new windows to maximum
- // if previous window was maximised
- desktop.setDesktopManager(new MyDesktopManager(
- (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
- : Platform.isAMacAndNotJS()
- ? new AquaInternalFrameManager(
- desktop.getDesktopManager())
- : desktop.getDesktopManager())));
+ // This line prevents Windows Look&Feel resizing all new windows to
+ // maximum
+ // if previous window was maximised
+ desktopPane.setDesktopManager(new MyDesktopManager(
+ (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
+ : Platform.isAMacAndNotJS()
+ ? new AquaInternalFrameManager(
+ desktopPane.getDesktopManager())
+ : desktopPane.getDesktopManager())));
- Rectangle dims = getLastKnownDimensions("");
- if (dims != null)
- {
- setBounds(dims);
- }
- else
- {
- Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
- int xPos = Math.max(5, (screenSize.width - 900) / 2);
- int yPos = Math.max(5, (screenSize.height - 650) / 2);
- setBounds(xPos, yPos, 900, 650);
- }
+ Rectangle dims = getLastKnownDimensions("");
+ if (dims != null)
+ {
+ setBounds(dims);
+ }
+ else
+ {
+ Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+ int xPos = Math.max(5, (screenSize.width - 900) / 2);
+ int yPos = Math.max(5, (screenSize.height - 650) / 2);
+ setBounds(xPos, yPos, 900, 650);
+ }
- if (!Platform.isJS())
- /**
- * Java only
- *
- * @j2sIgnore
- */
- {
- jconsole = new Console(this, showjconsole);
- jconsole.setHeader(Cache.getVersionDetailsForConsole());
- showConsole(showjconsole);
+ // Note that this next syntax, checking for Platform.isJS and also
+ // escaping the code using @j2sIgnore, serves two purposes. It gives
+ // us an easily findable tag, Platform.isJS(), to places in the code where
+ // there is something different about the SwingJS implementation. Second,
+ // it deletes the unneeded Java-only code form the JavaScript version
+ // completely (@j2sIgnore), since it will never be used there.
- showNews.setVisible(false);
+ if (!Platform.isJS() && !Jalview.isSynchronous())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
- experimentalFeatures.setSelected(showExperimental());
+ jconsole = new Console(this, showjconsole);
+ jconsole.setHeader(Cache.getVersionDetailsForConsole());
+ showConsole(showjconsole);
- getIdentifiersOrgData();
+ showNews.setVisible(false);
- checkURLLinks();
+ experimentalFeatures.setSelected(showExperimental());
- // Spawn a thread that shows the splashscreen
+ getIdentifiersOrgData();
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- new SplashScreen(true);
- }
- });
+ checkURLLinks();
- // Thread off a new instance of the file chooser - this reduces the time
- // it
- // takes to open it later on.
- new Thread(new Runnable()
- {
- @Override
- public void run()
+ // Spawn a thread that shows the splashscreen
+
+ SwingUtilities.invokeLater(new Runnable()
{
- Cache.log.debug("Filechooser init thread started.");
- String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
- JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
- fileFormat);
- Cache.log.debug("Filechooser init thread finished.");
- }
- }).start();
- // Add the service change listener
- changeSupport.addJalviewPropertyChangeListener("services",
- new PropertyChangeListener()
- {
+ @Override
+ public void run()
+ {
+ new SplashScreen(true);
+ }
+ });
- @Override
- public void propertyChange(PropertyChangeEvent evt)
+ // Thread off a new instance of the file chooser - this reduces the time
+ // it
+ // takes to open it later on.
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ Cache.log.debug("Filechooser init thread started.");
+ String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+ JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
+ fileFormat);
+ Cache.log.debug("Filechooser init thread finished.");
+ }
+ }).start();
+ // Add the service change listener
+ changeSupport.addJalviewPropertyChangeListener("services",
+ new PropertyChangeListener()
{
- Cache.log.debug("Firing service changed event for "
- + evt.getNewValue());
- JalviewServicesChanged(evt);
- }
- });
- }
- this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ Cache.log.debug("Firing service changed event for "
+ + evt.getNewValue());
+ JalviewServicesChanged(evt);
+ }
+
+ });
- this.addWindowListener(new WindowAdapter()
- {
- @Override
- public void windowClosing(WindowEvent evt)
- {
- quit();
}
- });
- MouseAdapter ma;
- this.addMouseListener(ma = new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
+ if (!Jalview.isSynchronous())
{
- if (evt.isPopupTrigger()) // Mac
+ this.setDropTarget(new java.awt.dnd.DropTarget(desktopPane, this));
+
+ this.addWindowListener(new WindowAdapter()
{
- showPasteMenu(evt.getX(), evt.getY());
- }
- }
+ @Override
+ public void windowClosing(WindowEvent evt)
+ {
+ quit();
+ }
+ });
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Windows
+ MouseAdapter ma;
+ this.addMouseListener(ma = new MouseAdapter()
{
- showPasteMenu(evt.getX(), evt.getY());
- }
- }
- });
- desktop.addMouseListener(ma);
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger()) // Mac
+ {
+ showPasteMenu(evt.getX(), evt.getY());
+ }
+ }
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger()) // Windows
+ {
+ showPasteMenu(evt.getX(), evt.getY());
+ }
+ }
+ });
+ desktopPane.addMouseListener(ma);
+ }
+ } catch (Throwable t)
+ {
+ t.printStackTrace();
+ }
}
/**
showNews(showNews.isSelected());
}
- void showNews(boolean visible)
+ protected void showNews(boolean visible)
{
Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
showNews.setSelected(visible);
public void run()
{
long now = System.currentTimeMillis();
- Desktop.instance.setProgressBar(
+ setProgressBar(
MessageManager.getString("status.refreshing_news"), now);
jvnews.refreshNews();
- Desktop.instance.setProgressBar(null, now);
+ setProgressBar(null, now);
jvnews.showNews();
}
}).start();
return null;
}
- void showPasteMenu(int x, int y)
+ protected void showPasteMenu(int x, int y)
{
JPopupMenu popup = new JPopupMenu();
JMenuItem item = new JMenuItem(
int w, int h, boolean resizable, boolean ignoreMinSize)
{
+
// TODO: allow callers to determine X and Y position of frame (eg. via
// bounds object).
// TODO: consider fixing method to update entries in the window submenu with
// the current window title
frame.setTitle(title);
- if (frame.getWidth() < 1 || frame.getHeight() < 1)
+ // BH fix
+ if (w > 0 && (frame.getWidth() < 1 || frame.getHeight() < 1))
{
frame.setSize(w, h);
}
// A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
// IF JALVIEW IS RUNNING HEADLESS
// ///////////////////////////////////////////////
- if (instance == null || (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true")))
+ if (Jalview.isHeadlessMode())
{
return;
}
frame.setIconifiable(resizable);
frame.setOpaque(Platform.isJS());
- if (frame.getX() < 1 && frame.getY() < 1)
+ boolean isEmbedded = (Platform.getDimIfEmbedded(frame, -1, -1) != null);
+ if (!isEmbedded && frame.getX() < 1 && frame.getY() < 1)
{
frame.setLocation(xOffset * openFrameCount,
yOffset * ((openFrameCount - 1) % 10) + yOffset);
* add an entry for the new frame in the Window menu
* (and remove it when the frame is closed)
*/
- final JMenuItem menuItem = new JMenuItem(title);
+ JMenuItem menuItem = new JMenuItem(title);
frame.addInternalFrameListener(new InternalFrameAdapter()
{
@Override
public void internalFrameActivated(InternalFrameEvent evt)
{
- JInternalFrame itf = desktop.getSelectedFrame();
+ JInternalFrame itf = getDesktopPane().getSelectedFrame();
if (itf != null)
{
if (itf instanceof AlignFrame)
{
menuItem.removeActionListener(menuItem.getActionListeners()[0]);
}
- windowMenu.remove(menuItem);
+ Desktop.getInstance().windowMenu.remove(menuItem);
}
});
setKeyBindings(frame);
- desktop.add(frame);
+ getDesktopPane().add(frame);
- windowMenu.add(menuItem);
+ Desktop.getInstance().windowMenu.add(menuItem);
frame.toFront();
try
{
if (!internalCopy)
{
- Desktop.jalviewClipboard = null;
+ Desktop.getInstance().jalviewClipboard = null;
}
internalCopy = false;
{
String msg = MessageManager
.formatMessage("label.couldnt_locate", url);
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+ msg,
MessageManager.getString("label.url_not_found"),
JvOptionPane.WARNING_MESSAGE);
};
String dialogOption = MessageManager
.getString("label.input_alignment_from_url");
- JvOptionPane.newOptionDialog(desktop).setResponseHandler(0, action)
+ JvOptionPane.newOptionDialog(getDesktopPane())
+ .setResponseHandler(0, action)
.showInternalDialog(panel, dialogOption,
JvOptionPane.YES_NO_CANCEL_OPTION,
JvOptionPane.PLAIN_MESSAGE, null, options,
@Override
public void run()
{
- new SplashScreen(false);
+ // BH! true meaning "interactive" here (applet branch); was false in develop version??
+ new SplashScreen(true);
}
}).start();
}
@Override
public void closeAll_actionPerformed(ActionEvent e)
{
+ if (desktopPane == null)
+ {
+ return;
+ }
// TODO show a progress bar while closing?
- JInternalFrame[] frames = desktop.getAllFrames();
+ JInternalFrame[] frames = desktopPane.getAllFrames();
for (int i = 0; i < frames.length; i++)
{
try
* reset state of singleton objects as appropriate (clear down session state
* when all windows are closed)
*/
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(this);
- if (ssm != null)
- {
- ssm.resetAll();
- }
+ getStructureSelectionManager().resetAll();
}
@Override
@Override
protected void showMemusage_actionPerformed(ActionEvent e)
{
- desktop.showMemoryUsage(showMemusage.isSelected());
+ getDesktopPane().showMemoryUsage(showMemusage.isSelected());
}
/*
void reorderAssociatedWindows(boolean minimize, boolean close)
{
- JInternalFrame[] frames = desktop.getAllFrames();
+ JInternalFrame[] frames = getDesktopPane().getAllFrames();
if (frames == null || frames.length < 1)
{
return;
saveState_actionPerformed(true);
}
- private void setProjectFile(File choice)
+ protected void setProjectFile(File choice)
{
this.projectFile = choice;
}
{
try
{
- new Jalview2XML().loadJalviewAlign(choice);
+ // BH was String "choice" here but needs to be File object
+ new Jalview2XML().loadJalviewAlign(selectedFile);
} catch (OutOfMemoryError oom)
{
new OOMWarning("Whilst loading project from " + choice, oom);
{
Cache.log.error(
"Problems whilst loading project from " + choice, ex);
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.error_whilst_loading_project_from",
new Object[]
{
progressPanel = new JPanel(new GridLayout(1, 1));
totalProgressCount = 0;
- instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
+ getContentPane().add(progressPanel, BorderLayout.SOUTH);
}
JPanel thisprogress = new JPanel(new BorderLayout(10, 5));
JProgressBar progressBar = new JProgressBar();
((GridLayout) progressPanel.getLayout()).setRows(
((GridLayout) progressPanel.getLayout()).getRows() + 1);
++totalProgressCount;
- instance.validate();
+ validate();
return thisprogress;
}
*/
public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
{
- if (Desktop.desktop == null)
+ if (Desktop.getDesktopPane() == null)
{
// no frames created and in headless mode
// TODO: verify that frames are recoverable when in headless mode
public static AlignmentViewport[] getViewports(String sequenceSetId)
{
List<AlignmentViewport> viewp = new ArrayList<>();
- if (desktop != null)
+ if (getDesktopPane() != null)
{
AlignFrame[] frames = Desktop.getAlignFrames();
return;
}
+ // BH! not in applet branch
// FIXME: ideally should use UI interface API
FeatureSettings viewFeatureSettings = (af.featureSettings != null
&& af.featureSettings.isOpen())
for (int i = 0; i < size; i++)
{
AlignmentPanel ap = af.alignPanels.get(i);
-
AlignFrame newaf = new AlignFrame(ap);
+ // BH! not in applet branch
// transfer reference for existing feature settings to new alignFrame
if (ap == af.alignPanel)
{
addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
+ // BH! not in applet branch
// and materialise a new feature settings dialog instance for the new alignframe
// (closes the old as if 'OK' was pressed)
if (ap == af.alignPanel && newaf.featureSettings != null
}
}
+ // BH! not in applet branch
af.featureSettings = null;
af.alignPanels.clear();
af.closeMenuItem_actionPerformed(true);
{
source.viewport.setGatherViewsHere(true);
source.viewport.setExplodedGeometry(source.getBounds());
- JInternalFrame[] frames = desktop.getAllFrames();
+ JInternalFrame[] frames = getAllFrames();
String viewId = source.viewport.getSequenceSetId();
+
for (int t = 0; t < frames.length; t++)
{
if (frames[t] instanceof AlignFrame && frames[t] != source)
if (gatherThis)
{
- if (af.featureSettings != null && af.featureSettings.isOpen())
- {
- if (source.featureSettings == null)
+ if (af.featureSettings != null && af.featureSettings.isOpen())
{
- // preserve the feature settings geometry for this frame
- source.featureSettings = af.featureSettings;
- source.setFeatureSettingsGeometry(
- af.getFeatureSettingsGeometry());
- }
- else
- {
- // close it and forget
- af.featureSettings.close();
+ if (source.featureSettings == null)
+ {
+ // preserve the feature settings geometry for this frame
+ source.featureSettings = af.featureSettings;
+ source.setFeatureSettingsGeometry(
+ af.getFeatureSettingsGeometry());
+ }
+ else
+ {
+ // close it and forget
+ af.featureSettings.close();
+ }
}
+ af.alignPanels.clear();
+ af.closeMenuItem_actionPerformed(true);
}
- af.alignPanels.clear();
- af.closeMenuItem_actionPerformed(true);
}
}
- }
-
// refresh the feature setting UI for the source frame if it exists
if (source.featureSettings != null
&& source.featureSettings.isOpen())
public JInternalFrame[] getAllFrames()
{
- return desktop.getAllFrames();
+ return desktopPane.getAllFrames();
}
/**
while (li.hasNext())
{
String link = li.next();
- if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID)
+ if (link.contains(UrlConstants.SEQUENCE_ID)
&& !UrlConstants.isDefaultString(link))
{
check = true;
});
msgPanel.add(jcb);
- JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel,
+ JvOptionPane.showMessageDialog(desktopPane, msgPanel,
MessageManager
.getString("label.SEQUENCE_ID_no_longer_used"),
JvOptionPane.WARNING_MESSAGE);
{
if (Jalview.isHeadlessMode())
{
- // Desktop.desktop is null in headless mode
- return new AlignFrame[] { Jalview.currentAlignFrame };
+ // Desktop.getDesktopPane() is null in headless mode
+ return new AlignFrame[] { Jalview.getCurrentAlignFrame() };
}
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
if (frames == null)
{
*/
public GStructureViewer[] getJmols()
{
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
if (frames == null)
{
} catch (Exception ex)
{
Cache.log.error("Groovy Shell Creation failed.", ex);
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(desktopPane,
MessageManager.getString("label.couldnt_create_groovy_shell"),
MessageManager.getString("label.groovy_support_failed"),
/**
* Open the Groovy console
*/
- void openGroovyConsole()
+ private void openGroovyConsole()
{
if (groovyConsole == null)
{
{
getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
.put(KeyStroke.getKeyStroke(KeyEvent.VK_Q,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()),
+ ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()),
"Quit");
getRootPane().getActionMap().put("Quit", new AbstractAction()
{
@Override
public void setProgressBar(String message, long id)
{
- // Platform.timeCheck("Desktop " + message, Platform.TIME_MARK);
+ // Platform.timeCheck("Desktop " + message, Platform.TIME_MARK);
if (progressBars == null)
{
*/
public static AlignFrame getAlignFrameFor(AlignViewportI viewport)
{
- if (desktop != null)
+ if (getDesktopPane() != null)
{
AlignmentPanel[] aps = getAlignmentPanels(
viewport.getSequenceSetId());
return null;
}
- public VamsasApplication getVamsasApplication()
- {
- // TODO: JAL-3311 remove remaining code from Jalview relating to VAMSAS
- return null;
-
- }
-
/**
* flag set if jalview GUI is being operated programmatically
*/
// todo: changesupport handlers need to be transferred
if (discoverer == null)
{
- discoverer = new jalview.ws.jws1.Discoverer();
- // register PCS handler for desktop.
+ discoverer = jalview.ws.jws1.Discoverer.getInstance();
+ // register PCS handler for getDesktopPane().
discoverer.addPropertyChangeListener(changeSupport);
}
// JAL-940 - disabled JWS1 service configuration - always start discoverer
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+ t2 = jalview.ws.jws2.Jws2Discoverer.getInstance()
.startDiscoverer(changeSupport);
}
Thread t3 = null;
{
if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
{
- final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+ final String ermsg = jalview.ws.jws2.Jws2Discoverer.getInstance()
.getErrorMessages();
if (ermsg != null)
{
*
* jd.waitForInput();
*/
- JvOptionPane.showConfirmDialog(Desktop.desktop,
+ JvOptionPane.showConfirmDialog(Desktop.getDesktopPane(),
new JLabel("<html><table width=\"450\"><tr><td>"
+ ermsg + "</td></tr></table>"
+ "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
}
}
- private Runnable serviceChangedDialog = null;
+ Runnable serviceChangedDialog = null;
/**
* start a thread to open a URL in the configured browser. Pops up a warning
*/
public static void showUrl(final String url)
{
- showUrl(url, Desktop.instance);
+ showUrl(url, Desktop.getInstance());
}
/**
{
try
{
- if (progress != null)
+ if (progress != null && !Platform.isJS())
{
progress.setProgressBar(MessageManager
.formatMessage("status.opening_params", new Object[]
{ url }), this.hashCode());
}
- jalview.util.BrowserLauncher.openURL(url);
+ Platform.openURL(url);
} catch (Exception ex)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager
.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
ex.printStackTrace();
}
- if (progress != null)
+ if (progress != null && !Platform.isJS())
{
progress.setProgressBar(null, this.hashCode());
}
}).start();
}
- public static WsParamSetManager wsparamManager = null;
+ private WsParamSetManager wsparamManager = null;
public static ParamManager getUserParameterStore()
{
- if (wsparamManager == null)
+ Desktop d = Desktop.getInstance();
+ if (d.wsparamManager == null)
{
- wsparamManager = new WsParamSetManager();
+ d.wsparamManager = new WsParamSetManager();
}
- return wsparamManager;
+ return d.wsparamManager;
}
/**
*/
private java.util.concurrent.Semaphore block = new Semaphore(0);
- private static groovy.ui.Console groovyConsole;
+ // BH was static
+ private groovy.ui.Console groovyConsole;
+
+ public StructureViewer lastTargetedView;
/**
* add another dialog thread to the queue
{
}
}
- if (instance == null)
+ // BH! Q: do we mean System.headless ? or "nogui/nodisplay" headless?
+ if (Jalview.isHeadlessMode())
{
return;
}
String topViewId = myTopFrame.viewport.getSequenceSetId();
String bottomViewId = myBottomFrame.viewport.getSequenceSetId();
- JInternalFrame[] frames = desktop.getAllFrames();
+ JInternalFrame[] frames = desktopPane.getAllFrames();
for (JInternalFrame frame : frames)
{
if (frame instanceof SplitFrame && frame != source)
public static groovy.ui.Console getGroovyConsole()
{
- return groovyConsole;
+ Desktop desktop = Desktop.getInstance();
+ return desktop == null ? null : desktop.groovyConsole;
}
/**
* - the payload from the drop event
* @throws Exception
*/
+ @SuppressWarnings("unchecked")
public static void transferFromDropTarget(List<Object> files,
List<DataSourceType> protocols, DropTargetDropEvent evt,
Transferable t) throws Exception
{
// Works on Windows and MacOSX
Cache.log.debug("Drop handled as javaFileListFlavor");
- for (Object file : (List) t
+ for (Object file : (List<Object>) t
.getTransferData(DataFlavor.javaFileListFlavor))
{
files.add(file);
Class<? extends StructureViewerBase> structureViewerClass)
{
List<StructureViewerBase> result = new ArrayList<>();
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
+ JInternalFrame[] frames = getAllFrames();
for (JInternalFrame frame : frames)
{
}
return result;
}
+
+
+
+ public MyDesktopPane desktopPane;
+
+ /**
+ * Get the instance of the JDesktopPane from the application-local Desktop
+ * (JFrame) instance
+ *
+ * The key here is that the Java application can have multiple static
+ * instances of the desktop JFrame because those instances are sandboxed, but
+ * the SwingJS JFrames will be in the same VM-like space. So we need
+ * application singletons, at least for JavaScript.
+ *
+ * @return
+ */
+ public static MyDesktopPane getDesktopPane()
+ {
+ Desktop desktop = Desktop.getInstance();
+ return desktop == null ? null : desktop.desktopPane;
+ }
+
+ /**
+ * Answers an 'application scope' singleton instance of this class. Separate
+ * SwingJS 'applets' running in the same browser page will each have a
+ * distinct instance of Desktop.
+ *
+ * @return
+ */
+ public static Desktop getInstance()
+ {
+ return Jalview.isHeadlessMode() ? null
+ : (Desktop) ApplicationSingletonProvider
+ .getInstance(Desktop.class);
+ }
+
}
updateColourButton(mainPanel, colour, featureColour);
};
};
- JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
+ JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(),
title, featureColour.getColour(), listener);
}
else
* set dialog action handlers for OK (create/Amend) and Cancel options
* also for Delete if applicable (when amending features)
*/
- JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
+ JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane())
.setResponseHandler(0, okAction).setResponseHandler(2, cancelAction);
if (!forCreate)
{
package jalview.gui;
/**
- * A class that manages drawing of sequence features for the Swing gui
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
*/
public class FeatureRenderer
extends jalview.renderer.seqfeatures.FeatureRenderer
+ implements jalview.api.FeatureRenderer
{
AlignmentPanel ap;
{
super(alignPanel.av);
this.ap = alignPanel;
- if (alignPanel.getSeqPanel() != null
- && alignPanel.getSeqPanel().seqCanvas != null
- && alignPanel.getSeqPanel().seqCanvas.fr != null)
+ SeqPanel sp = alignPanel.getSeqPanel();
+ if (sp != null && sp.seqCanvas != null && sp.seqCanvas.fr != null)
{
- transferSettings(alignPanel.getSeqPanel().seqCanvas.fr);
+ transferSettings(sp.seqCanvas.fr);
}
}
}
}
else
{
- frame = new JInternalFrame();
- frame.setContentPane(this);
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
Rectangle bounds = af.getFeatureSettingsGeometry();
String title;
if (af.getAlignPanels().size() > 1 || Desktop.getAlignmentPanels(
frame.setBounds(bounds);
frame.setVisible(true);
}
- frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
- frame.addInternalFrameListener(
- new javax.swing.event.InternalFrameAdapter()
+ frame.addInternalFrameListener(
+ new javax.swing.event.InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
{
- @Override
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
featureSettings_isClosed();
};
- });
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ });
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
}
- inConstruction = false;
- }
+ inConstruction = false;
+ }
/**
* Sets the state of buttons to show complement features from viewport
/**
* Constructs and shows a popup menu of possible actions on the selected row and
* feature type
- *
- * @param rowSelected
- * @param type
- * @param typeCol
- * @param pt
- */
+ *
+ * @param rowSelected
+ * @param type
+ * @param typeCol
+ * @param pt
+ */
protected void showPopupMenu(final int rowSelected, final String type, final Object typeCol, final Point pt)
{
JPopupMenu men = new JPopupMenu(MessageManager
{
if (e.getSource() == variableColourCB)
{
- // BH 2018 for JavaScript because this is a checkbox
- men.setVisible(true);
+ // BH 2018 for JavaScript because this is a checkbox
+ men.setVisible(true);
men.setVisible(false);
if (featureColour.isSimpleColour())
{
men.add(scr);
scr.addActionListener(new ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
MessageManager.getString("label.sort_by_density"));
dens.addActionListener(new ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
if (frame != null)
{
af.setFeatureSettingsGeometry(frame.getBounds());
- frame.setClosed(true);
+ frame.setClosed(true);
}
else
{
{
if (!hasComplement)
{
- close();
- }
+ close();
+ }
else
{
storeOriginalSettings();
*
* @param fcol
* @param withHint
- * if true include 'click to edit' and similar text
+ * if true include 'click to edit' and similar text
* @return
*/
public static String getColorTooltip(FeatureColourI fcol,
*/
boolean getFocusedViewport()
{
- if (focusfixed || Desktop.desktop == null)
+ if (focusfixed || Desktop.getDesktopPane() == null)
{
if (ap != null && av != null)
{
}
// now checks further down the window stack to fix bug
// https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
for (int f = 0; f < frames.length; f++)
{
JInternalFrame alignFrame = frames[f];
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
JvOptionPane.WARNING_MESSAGE);
PopupMenu pop = new PopupMenu(alignPanel, sq,
Preferences.getGroupURLLinks());
pop.show(this, e.getX(), e.getY());
+ }
}
- }
/**
* On right mouse click on a Consensus annotation label, shows a limited popup
boolean block, String title, int width, int height)
{
- frame = new JDialog(Desktop.instance, modal);
+ frame = new JDialog(Desktop.getInstance(), modal);
frame.setTitle(title);
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
- Rectangle deskr = Desktop.instance.getBounds();
+ Rectangle deskr = Desktop.getInstance().getBounds();
frame.setBounds(new Rectangle((int) (deskr.getCenterX() - width / 2),
(int) (deskr.getCenterY() - height / 2), width, height));
}
*/
package jalview.gui;
+import jalview.util.MessageManager;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
*/
public final class JvSwingUtils
{
+ static final String HTML_PREFIX = "<html><div style=\"width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;\">";
+
/**
* wrap a bare html safe string to around 60 characters per line using a CSS
* style class specifying word-wrap and break-word
*
* @param enclose
- * if true, add <html> wrapper tags
+ * if true, add <html> wrapper tags (currently false for only
+ * two references -- both in Jws2Discoverer --
* @param ttext
*
* @return
{
return enclose ? "<html>" + ttext + "</html>" : ttext;
}
+ // BH 2018,2019
+ return (enclose ? HTML_PREFIX + ttext + "</div></html>" : ttext);
- return (enclose ? "<html>" : "")
- // BH 2018
- + "<style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style><div class=\"ttip\">"
-// + "<style> p.ttip {width:350px;margin:-14px 0px -14px 0px;padding:2px;overflow-wrap:break-word;}"
-// + "</style><p class=\"ttip\">"
- + ttext
- + " </div>"
-// + "</p>"
- + ((enclose ? "</html>" : ""));
}
public static JButton makeButton(String label, String tooltip,
combo.setToolTipText(tooltips.get(j));
}
}
+
@Override
public void mouseExited(MouseEvent e)
{
ex.printStackTrace();
}
- dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
+ dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane());
}
/**
}
else
{
- Cache.applicationProperties.remove(preferencesKey);
+ Cache.removePropertyNoSave(preferencesKey);
}
}
public OOMWarning(String string, OutOfMemoryError oomerror)
{
- this(string, oomerror, Desktop.desktop);
+ this(string, oomerror, Desktop.getDesktopPane());
}
@Override
{
try
{
- jalview.util.BrowserLauncher.openURL(url);
+ Platform.openURL(url);
} catch (Exception ex)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
JvOptionPane.WARNING_MESSAGE);
if (forIdPanel)
{
- JMenuItem menuItem;
+ JMenuItem menuItem;
sequenceMenu.setText(sequence.getName());
if (seq == alignPanel.av.getAlignment().getSeqrep())
{
/*
* add features in CDS/protein complement at the corresponding
* position if configured to do so
- */
+ */
MappedFeatures mf = null;
if (ap.av.isShowComplementFeatures())
{
if (!Comparison.isGap(sequence.getCharAt(column)))
- {
+ {
AlignViewportI complement = ap.getAlignViewport()
.getCodingComplement();
AlignFrame af = Desktop.getAlignFrameFor(complement);
*/
return;
}
-
JMenu details = new JMenu(
MessageManager.getString("label.feature_details"));
add(details);
void addFeatureDetailsMenuItem(JMenu details, final String seqName,
final SequenceFeature sf)
{
- int start = sf.getBegin();
- int end = sf.getEnd();
+ int start = sf.getBegin();
+ int end = sf.getEnd();
StringBuilder desc = new StringBuilder();
desc.append(sf.getType()).append(" ").append(String.valueOf(start));
if (start != end)
- {
+ {
desc.append("-").append(String.valueOf(end));
- }
- String description = sf.getDescription();
- if (description != null)
- {
+ }
+ String description = sf.getDescription();
+ if (description != null)
+ {
desc.append(" ");
- description = StringUtils.stripHtmlTags(description);
+ description = StringUtils.stripHtmlTags(description);
/*
* truncate overlong descriptions unless they contain an href
*/
boolean hasLink = description.indexOf("a href") > -1;
if (description.length() > FEATURE_DESC_MAX && !hasLink)
- {
+ {
description = description.substring(0, FEATURE_DESC_MAX) + "...";
- }
+ }
desc.append(description);
- }
+ }
String featureGroup = sf.getFeatureGroup();
if (featureGroup != null)
- {
+ {
desc.append(" (").append(featureGroup).append(")");
- }
+ }
String htmlText = JvSwingUtils.wrapTooltip(true, desc.toString());
JMenuItem item = new JMenuItem(htmlText);
- item.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
+ item.addActionListener(new ActionListener()
{
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
showFeatureDetails(seqName, sf);
- }
- });
- details.add(item);
- }
+ }
+ });
+ details.add(item);
+ }
/**
* Opens a panel showing a text report of feature dteails
groupLinksMenu.add(linkMenus[m]);
}
}
-
groupMenu.add(groupLinksMenu);
}
}
{
JMenuItem hideInsertions = new JMenuItem(
MessageManager.getString("label.hide_insertions"));
- hideInsertions.addActionListener(new ActionListener()
- {
+ hideInsertions.addActionListener(new ActionListener()
+ {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hideInsertions_actionPerformed(e);
- }
- });
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideInsertions_actionPerformed(e);
+ }
+ });
add(hideInsertions);
}
// annotations configuration panel suppressed for now
getGroup().setOutlineColour(c);
refresh();
}
- };
- JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
+ };
+ JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(),
title, Color.BLUE, listener);
}
}
try
{
- int reply = JvOptionPane.showConfirmDialog(Desktop.desktop, // component,
+ int reply = JvOptionPane.showConfirmDialog(Desktop.getDesktopPane(), // component,
dialogText, dialogTitle,
(allowCancel) ? JvOptionPane.YES_NO_CANCEL_OPTION
: JvOptionPane.YES_NO_OPTION,
import javax.swing.ToolTipManager;
/**
- * DOCUMENT ME!
+ * The main scrollable region containing the alignment and just to the right of
+ * the IDPanel.
*
* @author $author$
* @version $Revision: 1.130 $
MousePos o = (MousePos) obj;
boolean b = (column == o.column && seqIndex == o.seqIndex
&& annotationIndex == o.annotationIndex);
- // System.out.println(obj + (b ? "= " : "!= ") + this);
return b;
}
return;
}
- // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
// Selection spans a hidden region
if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
{
{
lastMousePosition = null;
ap.alignFrame.setStatus(" ");
+
if (av.getWrapAlignment())
{
return;
}
+ // BH check was:
+// /*
+// * start scrolling if mouse dragging, whether the drag started
+// * in the scale panel or this panel
+// */
+// if (mouseDragging || ap.getScalePanel().isMouseDragging())
+// {
+// startScrolling(new Point(e.getX(), 0));
+// }
+
if (mouseDragging && scrollThread == null)
{
startScrolling(e.getPoint());
if (sequence != null)
{
PopupMenu pop = new PopupMenu(ap, sequence, column);
- pop.show(this, evt.getX(), evt.getY());
- }
+ pop.show(this, evt.getX(), evt.getY());
+ }
}
/**
* Map sequence selection
*/
SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
- av.setSelectionGroup(sg != null && sg.getSize() > 0 ? sg : null);
+ av.setSelectionGroup(sg);
av.isSelectionGroupChanged(true);
/*
{
return lastSearchResults;
}
+
+ /**
+ * scroll to the given row/column - or nearest visible location
+ *
+ * @param row
+ * @param column
+ */
+ public void scrollTo(int row, int column)
+ {
+
+ row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
+ column = column < 0 ? ap.av.getRanges().getStartRes() : column;
+ ap.scrollTo(column, column, row, true, true);
+ }
+
+ /**
+ * scroll to the given row - or nearest visible location
+ *
+ * @param row
+ */
+ public void scrollToRow(int row)
+ {
+
+ row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
+ ap.scrollTo(ap.av.getRanges().getStartRes(),
+ ap.av.getRanges().getStartRes(), row, true, true);
+ }
+
+ /**
+ * scroll to the given column - or nearest visible location
+ *
+ * @param column
+ */
+ public void scrollToColumn(int column)
+ {
+
+ column = column < 0 ? ap.av.getRanges().getStartRes() : column;
+ ap.scrollTo(column, column, ap.av.getRanges().getStartSeq(), true,
+ true);
+ }
+
}
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, error,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), error,
MessageManager.getString("label.error_retrieving_data"),
JvOptionPane.WARNING_MESSAGE);
}
System.err.println("Error when loading images!");
}
} while (!mt.checkAll());
- Desktop.instance.setIconImage(logo);
+ Desktop.getInstance().setIconImage(logo);
}
} catch (Exception ex)
{
}
add(splashText, BorderLayout.CENTER);
splashText.addMouseListener(closer);
- Desktop.desktop.add(iframe);
+ Desktop.getDesktopPane().add(iframe);
refreshText();
}
*/
protected boolean refreshText()
{
- String newtext = Desktop.instance.getAboutMessage();
+ String newtext = Desktop.getInstance().getAboutMessage();
// System.err.println("Text found: \n"+newtext+"\nEnd of newtext.");
if (oldTextLength != newtext.length())
{
splashText.setSize(new Dimension(750, 375));
add(splashText, BorderLayout.CENTER);
revalidate();
- iframe.setBounds((Desktop.instance.getWidth() - 750) / 2,
- (Desktop.instance.getHeight() - 375) / 2, 750,
+ iframe.setBounds((Desktop.getInstance().getWidth() - 750) / 2,
+ (Desktop.getInstance().getHeight() - 375) / 2, 750,
splashText.getHeight() + iconimg.getHeight());
iframe.validate();
iframe.setVisible(true);
}
closeSplash();
- Desktop.instance.startDialogQueue();
+ Desktop.getInstance().startDialogQueue();
}
/**
// allow about 65 pixels for Desktop decorators on Windows
int newHeight = Math.min(height,
- Desktop.instance.getHeight() - DESKTOP_DECORATORS_HEIGHT);
+ Desktop.getInstance().getHeight() - DESKTOP_DECORATORS_HEIGHT);
if (newHeight != height)
{
int oldDividerLocation = getDividerLocation();
{
// TODO if CommandListener is only ever 1:1 for complementary views,
// may change broadcast pattern to direct messaging (more efficient)
- final StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ final StructureSelectionManager ssm = Desktop
+ .getStructureSelectionManager();
ssm.addCommandListener(((AlignFrame) getTopFrame()).getViewport());
ssm.addCommandListener(((AlignFrame) getBottomFrame()).getViewport());
}
public void internalFrameClosed(InternalFrameEvent evt)
{
close();
- };
+ }
});
}
*/
adjustLayout();
- final StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ final StructureSelectionManager ssm = Desktop
+ .getStructureSelectionManager();
ssm.addCommandListener(newTopPanel.av);
ssm.addCommandListener(newBottomPanel.av);
}
*/
protected void expandViews_actionPerformed()
{
- Desktop.instance.explodeViews(this);
+ Desktop.getInstance().explodeViews(this);
}
/**
*/
protected void gatherViews_actionPerformed()
{
- Desktop.instance.gatherViews(this);
+ Desktop.getInstance().gatherViews(this);
}
/**
return;
}
getAlignFrames().get(tab).showFeatureSettingsUI();
- }
+}
});
featureSettingsUI = new JInternalFrame(MessageManager.getString(
"label.sequence_feature_settings_for_CDS_and_Protein"));
1);
}
featureSettingsPanels.setSelectedComponent((Component) featureSettings);
-
// TODO: JAL-3535 - construct a feature settings title including names of
// currently selected CDS and Protein names
*/
private void discoverStructureViews()
{
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
targetView.removeAllItems();
if (lastTargetedView != null && !lastTargetedView.isVisible())
lastTargetedView = null;
}
int linkedViewsAt = 0;
- for (StructureViewerBase view : Desktop.instance
+ for (StructureViewerBase view : Desktop.getInstance()
.getStructureViewers(null, null))
{
StructureViewer viewHandler = (lastTargetedView != null
PDBEntry fileEntry = new AssociatePdbFileWithSeq()
.associatePdbWithSeq(selectedPdbFileName,
DataSourceType.FILE, selectedSequence, true,
- Desktop.instance);
+ Desktop.getInstance());
sViewer = launchStructureViewer(
ssm, new PDBEntry[]
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.StructureViewerModel;
+import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.sifts.SiftsSettings;
import java.awt.Rectangle;
import java.util.ArrayList;
*/
public class StructureViewer
{
+
+ static
+ {
+ Platform.ensureJmol();
+ }
+
private static final String UNKNOWN_VIEWER_TYPE = "Unknown structure viewer type ";
StructureSelectionManager ssm;
public enum ViewerType
{
JMOL, CHIMERA
- };
+ }
/**
* Constructor
superposeAdded = alignAddedStructures;
}
+ /**
+ * Launch a minimal implementation of a StructureViewer.
+ *
+ * @param alignPanel
+ * @param pdb
+ * @param seqs
+ * @return
+ */
+ public static StructureViewer launchStructureViewer(
+ AlignmentPanel alignPanel, PDBEntry pdb, SequenceI[] seqs)
+ {
+ return launchStructureViewer(alignPanel, new PDBEntry[] { pdb }, seqs,
+ false, null, null);
+ }
+
+ /**
+ * Launch a structure viewer with or without an open StructureChooser.
+ *
+ * Moved from StructureChooser to enable JalviewJS startup with structure
+ * display.
+ *
+ * @param ap
+ * @param pdbEntriesToView
+ * @param sequences
+ * @param superimpose
+ * @param theViewer
+ * @param pb
+ * @return
+ */
+ protected static StructureViewer launchStructureViewer(
+ final AlignmentPanel ap,
+ final PDBEntry[] pdbEntriesToView, SequenceI[] sequences,
+ boolean superimpose, StructureViewer theViewer,
+ IProgressIndicator pb)
+ {
+ final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+ long progressId = sequences.hashCode();
+ if (pb != null)
+ {
+ pb.setProgressBar(MessageManager
+ .getString("status.launching_3d_structure_viewer"), progressId);
+ }
+ if (theViewer == null)
+ {
+ theViewer = new StructureViewer(ssm);
+ }
+ theViewer.setSuperpose(superimpose);
+
+ if (pb != null)
+ {
+ pb.setProgressBar(null, progressId);
+ }
+ if (SiftsSettings.isMapWithSifts())
+ {
+ List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
+ int p = 0;
+ // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
+ // real PDB ID. For moment, we can also safely do this if there is already
+ // a known mapping between the PDBEntry and the sequence.
+ for (SequenceI seq : sequences)
+ {
+ PDBEntry pdbe = pdbEntriesToView[p++];
+ if (pdbe != null && pdbe.getFile() != null)
+ {
+ StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
+ if (smm != null && smm.length > 0)
+ {
+ for (StructureMapping sm : smm)
+ {
+ if (sm.getSequence() == seq)
+ {
+ continue;
+ }
+ }
+ }
+ }
+ if (seq.getPrimaryDBRefs().isEmpty())
+ {
+ seqsWithoutSourceDBRef.add(seq);
+ continue;
+ }
+ }
+ if (!seqsWithoutSourceDBRef.isEmpty())
+ {
+ int y = seqsWithoutSourceDBRef.size();
+ if (pb != null)
+ {
+ pb.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_dbrefs_for_sequences_without_valid_refs",
+ y), progressId);
+ }
+ SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
+ .toArray(new SequenceI[y]);
+ DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
+ dbRefFetcher.fetchDBRefs(true);
+
+ if (pb != null)
+ {
+ pb.setProgressBar("Fetch complete.", progressId); // todo i18n
+ }
+ }
+ }
+ if (pdbEntriesToView.length > 1)
+ {
+ if (pb != null)
+ {
+ pb.setProgressBar(MessageManager.getString(
+ "status.fetching_3d_structures_for_selected_entries"),
+ progressId);
+ }
+ theViewer.viewStructures(pdbEntriesToView, sequences, ap);
+ }
+ else
+ {
+ if (pb != null)
+ {
+ pb.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_3d_structures_for",
+ pdbEntriesToView[0].getId()),progressId);
+ }
+ theViewer.viewStructures(pdbEntriesToView[0], sequences, ap);
+ }
+ if (pb != null)
+ {
+ pb.setProgressBar(null, progressId);
+ }
+ // remember the last viewer we used...
+ Desktop.getInstance().lastTargetedView = theViewer;
+ return theViewer;
+ }
+
}
*/
protected List<StructureViewerBase> getViewersFor(AlignmentPanel alp)
{
- return Desktop.instance.getStructureViewers(alp, this.getClass());
+ return Desktop.getInstance().getStructureViewers(alp, this.getClass());
}
@Override
{
if (isNoSelectionMade())
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
MessageManager
.getString("label.no_colour_selection_in_scheme"),
MessageManager.getString("label.no_colour_selection_warn"),
String[] options = new String[] { title,
MessageManager.getString("label.dont_save_changes"), };
final String question = JvSwingUtils.wrapTooltip(true, message);
- int response = JvOptionPane.showOptionDialog(Desktop.desktop,
+ int response = JvOptionPane.showOptionDialog(Desktop.getDesktopPane(),
question, title, JvOptionPane.DEFAULT_OPTION,
JvOptionPane.PLAIN_MESSAGE, null, options, options[0]);
{
if (isNoSelectionMade())
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
MessageManager
.getString("label.no_colour_selection_in_scheme"),
MessageManager.getString("label.no_colour_selection_warn"),
String name = schemeName.getText().trim();
if (name.length() < 1)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager
.getString("label.user_colour_scheme_must_have_name"),
MessageManager.getString("label.no_name_colour_scheme"),
* @j2sIgnore
*/
{
- int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ int reply = JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.colour_scheme_exists_overwrite", new Object[]
{ name, name }),
+ qid + "&rid=" + rid;
jalview.bin.Cache.log
.info("Prompting user for questionnaire at " + qurl);
- int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ int reply = JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.jalview_new_questionnaire"),
MessageManager.getString("label.jalview_user_survey"),
JvOptionPane.YES_NO_OPTION, JvOptionPane.QUESTION_MESSAGE);
}
} catch (InvalidSessionDocumentException e)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString(
"label.vamsas_doc_couldnt_be_opened_as_new_session"),
VamsasAppDatastore vds = new VamsasAppDatastore(doc, vobj2jv, jv2vobj,
baseProvEntry(), alRedoState);
// wander through frames
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
if (frames == null)
{
Cache.log.debug(
"Asking user if the vamsas session should be stored.");
int reply = JvOptionPane.showInternalConfirmDialog(
- Desktop.desktop,
+ Desktop.getDesktopPane(),
"The current VAMSAS session has unsaved data - do you want to save it ?",
"VAMSAS Session Shutdown",
JvOptionPane.YES_NO_OPTION,
if (reply == JvOptionPane.YES_OPTION)
{
Cache.log.debug("Prompting for vamsas store filename.");
- Desktop.instance.vamsasSave_actionPerformed(null);
+ Desktop.getInstance().vamsasSave_actionPerformed(null);
Cache.log
.debug("Finished attempt at storing document.");
}
}
try
{
- final IPickManager pm = vclient.getPickManager();
- final StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- final VamsasApplication me = this;
+ IPickManager pm = vclient.getPickManager();
+ StructureSelectionManager ssm = Desktop
+ .getStructureSelectionManager();
+ VamsasApplication me = this;
pm.registerMessageHandler(new IMessageHandler()
{
String last = null;
{
type = jvobjs[o].getClass();
}
- ;
if (type != jvobjs[o].getClass())
{
send = false;
{
jvobjs[c] = null;
}
- ;
jvobjs = null;
return;
}
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, message,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), message,
title, JvOptionPane.WARNING_MESSAGE);
}
public boolean showRunDialog()
{
- frame = new JDialog(Desktop.instance, true);
+ frame = new JDialog(Desktop.getInstance(), true);
frame.setTitle(MessageManager.formatMessage("label.edit_params_for",
new String[]
{ service.getActionText() }));
- Rectangle deskr = Desktop.instance.getBounds();
+ Rectangle deskr = Desktop.getInstance().getBounds();
Dimension pref = this.getPreferredSize();
frame.setBounds(
new Rectangle((int) (deskr.getCenterX() - pref.width / 2),
dialogpanel.add(canceljob);
// JAL-1580: setMaximumSize() doesn't work, so just size for the worst case:
// check for null is for JUnit usage
- final int windowHeight = Desktop.instance == null ? 540
- : Desktop.instance.getHeight();
+ final int windowHeight = Desktop.getInstance() == null ? 540
+ : Desktop.getInstance().getHeight();
setPreferredSize(new Dimension(540, windowHeight));
add(dialogpanel, BorderLayout.SOUTH);
validate();
{
Vector<String> services = new Vector<>();
services.addElement(args[p++]);
- Jws2Discoverer.getDiscoverer().setServiceUrls(services);
+ Jws2Discoverer.getInstance().setServiceUrls(services);
}
try
{
chooser.setDialogTitle(MessageManager
.getString("label.choose_filename_for_param_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
- int value = chooser.showSaveDialog(Desktop.instance);
+ int value = chooser.showSaveDialog(Desktop.getInstance());
if (value == JalviewFileChooser.APPROVE_OPTION)
{
outfile = chooser.getSelectedFile();
File pfile = new File(filename);
if (pfile.exists() && pfile.canWrite())
{
- if (JvOptionPane.showConfirmDialog(Desktop.instance,
+ if (JvOptionPane.showConfirmDialog(Desktop.getInstance(),
"Delete the preset's file, too ?", "Delete User Preset ?",
JvOptionPane.OK_CANCEL_OPTION) == JvOptionPane.OK_OPTION)
{
private void initFromPreferences()
{
- wsUrls = Jws2Discoverer.getDiscoverer().getServiceUrls();
+ wsUrls = Jws2Discoverer.getInstance().getServiceUrls();
if (!wsUrls.isEmpty())
{
oldUrls = new Vector<String>(wsUrls);
int r = 0;
for (String url : wsUrls)
{
- int status = Jws2Discoverer.getDiscoverer().getServerStatusFor(url);
+ int status = Jws2Discoverer.getInstance().getServerStatusFor(url);
tdat[r][1] = Integer.valueOf(status);
tdat[r++][0] = url;
}
private void updateServiceList()
{
- Jws2Discoverer.getDiscoverer().setServiceUrls(wsUrls);
+ Jws2Discoverer.getInstance().setServiceUrls(wsUrls);
}
private void updateRsbsServiceList()
boolean valid = false;
int resp = JvOptionPane.CANCEL_OPTION;
while (!valid && (resp = JvOptionPane.showInternalConfirmDialog(
- Desktop.desktop, panel, title,
+ Desktop.getDesktopPane(), panel, title,
JvOptionPane.OK_CANCEL_OPTION)) == JvOptionPane.OK_OPTION)
{
try
} catch (Exception e)
{
valid = false;
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.invalid_url"));
}
}
if (valid && resp == JvOptionPane.OK_OPTION)
{
- int validate = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ int validate = JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(),
MessageManager.getString("info.validate_jabaws_server"),
MessageManager.getString("label.test_server"),
JvOptionPane.YES_NO_OPTION);
}
else
{
- int opt = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
+ int opt = JvOptionPane.showInternalOptionDialog(Desktop.getDesktopPane(),
"The Server '" + foo.toString()
+ "' failed validation,\ndo you want to add it anyway? ",
"Server Validation Failed", JvOptionPane.YES_NO_OPTION,
}
else
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString(
"warn.server_didnt_pass_validation"));
}
if (lastrefresh != update)
{
lastrefresh = update;
- Desktop.instance.startServiceDiscovery(true); // wait around for all
+ Desktop.getInstance().startServiceDiscovery(true); // wait around for all
// threads to complete
updateList();
public void run()
{
long ct = System.currentTimeMillis();
- Desktop.instance.setProgressBar(MessageManager
+ Desktop.getInstance().setProgressBar(MessageManager
.getString("status.refreshing_web_service_menus"), ct);
if (lastrefresh != update)
{
lastrefresh = update;
- Desktop.instance.startServiceDiscovery(true);
+ Desktop.getInstance().startServiceDiscovery(true);
updateList();
}
- Desktop.instance.setProgressBar(null, ct);
+ Desktop.getInstance().setProgressBar(null, ct);
}
}).start();
@Override
protected void resetWs_actionPerformed(ActionEvent e)
{
- Jws2Discoverer.getDiscoverer().setServiceUrls(null);
- List<String> nwsUrls = Jws2Discoverer.getDiscoverer().getServiceUrls();
+ Jws2Discoverer.getInstance().setServiceUrls(null);
+ List<String> nwsUrls = Jws2Discoverer.getInstance().getServiceUrls();
if (!wsUrls.equals(nwsUrls))
{
update++;
private static final String ID_NOT_SPECIFIED = "ID_NOT_SPECIFIED";
+ private static final String NOTE = "Note";
+
protected static final String GFF_VERSION = "##gff-version";
private AlignmentI lastmatchedAl = null;
.getDisplayedFeatureCols();
Map<String, FeatureMatcherSetI> featureFilters = fr.getFeatureFilters();
+ // BH check this is out?
+// if (!includeNonPositional
+// && (visibleColours == null || visibleColours.isEmpty()))
+// {
+// // no point continuing.
+// return "No Features Visible";
+// }
+
/*
* write out feature colours (if we know them)
*/
* @param sequenceName
* @param sequenceFeature
*/
- protected void formatJalviewFeature(
+ protected String formatJalviewFeature(
StringBuilder out, String sequenceName,
SequenceFeature sequenceFeature)
{
out.append(sequenceFeature.score);
}
out.append(newline);
+
+ return out.toString();
}
/**
AlignViewportI av = getViewport();
if (av != null)
{
- if (av.getAlignment() != null)
+ AlignmentI a = av.getAlignment();
+ if (a != null)
{
- dataset = av.getAlignment().getDataset();
+ dataset = a.getDataset();
}
if (dataset == null)
{
// working in the applet context ?
- dataset = av.getAlignment();
+ dataset = a;
}
}
else
* Returns features output in GFF2 format
*
* @param sequences
- * the sequences whose features are to be
- * output
+ * the sequences whose features are to be output
* @param visible
- * a map whose keys are the type names of
- * visible features
+ * a map whose keys are the type names of visible features
* @param visibleFeatureGroups
* @param includeNonPositionalFeatures
* @param includeComplement
{
FeatureRenderer fr2 = null;
if (includeComplement)
- {
+ {
AlignViewportI comp = fr.getViewport().getCodingComplement();
fr2 = Desktop.getAlignFrameFor(comp).getFeatureRenderer();
}
{
features.addAll(seq.getFeatures().getPositionalFeatures(types));
}
+
for (SequenceFeature sf : features)
{
if (sf.isNonPositional() || fr.isVisible(sf))
private void formatGffFeature(StringBuilder out, SequenceI seq,
SequenceFeature sf)
{
- String source = sf.featureGroup;
- if (source == null)
- {
- source = sf.getDescription();
- }
-
- out.append(seq.getName());
- out.append(TAB);
- out.append(source);
- out.append(TAB);
- out.append(sf.type);
- out.append(TAB);
- out.append(sf.begin);
- out.append(TAB);
- out.append(sf.end);
- out.append(TAB);
- out.append(sf.score);
- out.append(TAB);
-
- int strand = sf.getStrand();
- out.append(strand == 1 ? "+" : (strand == -1 ? "-" : "."));
- out.append(TAB);
+ String source = sf.featureGroup;
+ if (source == null)
+ {
+ source = sf.getDescription();
+ }
- String phase = sf.getPhase();
- out.append(phase == null ? "." : phase);
+ out.append(seq.getName());
+ out.append(TAB);
+ out.append(source);
+ out.append(TAB);
+ out.append(sf.type);
+ out.append(TAB);
+ out.append(sf.begin);
+ out.append(TAB);
+ out.append(sf.end);
+ out.append(TAB);
+ out.append(sf.score);
+ out.append(TAB);
+
+ int strand = sf.getStrand();
+ out.append(strand == 1 ? "+" : (strand == -1 ? "-" : "."));
+ out.append(TAB);
+
+ String phase = sf.getPhase();
+ out.append(phase == null ? "." : phase);
if (sf.otherDetails != null && !sf.otherDetails.isEmpty())
- {
+ {
Map<String, Object> map = sf.otherDetails;
formatAttributes(out, map);
}
* format)
*
* @param alignedRegions
- * a list of "Align fromStart toStart fromCount"
+ * a list of "Align fromStart toStart fromCount"
* @param mapIsFromCdna
- * if true, 'from' is dna, else 'from' is protein
+ * if true, 'from' is dna, else 'from' is protein
* @param strand
- * either 1 (forward) or -1 (reverse)
+ * either 1 (forward) or -1 (reverse)
* @return
* @throws IOException
*/
return seq;
}
+ // BH! check that we did not lose something here.
+// /**
+// * Process the 'column 9' data of the GFF file. This is less formally defined,
+// * and its interpretation will vary depending on the tool that has generated
+// * it.
+// *
+// * @param attributes
+// * @param sf
+// */
+// protected void processGffColumnNine(String attributes, SequenceFeature sf)
+// {
+// sf.setAttributes(attributes);
+//
+// /*
+// * Parse attributes in column 9 and add them to the sequence feature's
+// * 'otherData' table; use Note as a best proxy for description
+// */
+// char nameValueSeparator = gffVersion == 3 ? '=' : ' ';
+// // TODO check we don't break GFF2 values which include commas here
+// Map<String, List<String>> nameValues = GffHelperBase
+// .parseNameValuePairs(attributes, ";", nameValueSeparator, ",");
+// for (Entry<String, List<String>> attr : nameValues.entrySet())
+// {
+// String values = StringUtils.listToDelimitedString(attr.getValue(),
+// "; ");
+// sf.setValue(attr.getKey(), values);
+// if (NOTE.equals(attr.getKey()))
+// {
+// sf.setDescription(values);
+// }
+// }
+// }
+
/**
* After encountering ##fasta in a GFF3 file, process the remainder of the
* file as FAST sequence data. Any placeholder sequences created during
import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.project.Jalview2XML;
import jalview.schemes.ColourSchemeI;
-import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.utils.UrlDownloadClient;
+import java.awt.Dimension;
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStreamReader;
-import java.util.StringTokenizer;
-import java.util.Vector;
+import java.util.ArrayList;
+import java.util.List;
import javax.swing.SwingUtilities;
public class FileLoader implements Runnable
{
+ private static final String DEFAULT_FILE_FORMAT_PROPERTY = "DEFAULT_FILE_FORMAT";
+
+ private static final String RECENT_URL_PROPERTY = "RECENT_URL";
+
+ private static final String RECENT_FILE_PROPERTY = "RECENT_FILE";
+
+ private static final String TAB = "\t";
+
+ /*
+ * maximum number of items in file/url history lists;
+ * pseudo-constant (not final) so amendable by Groovy if wanted
+ */
+ private static int MAX_HISTORY = 11;
+
String file;
DataSourceType protocol;
FileFormatI format;
- AlignmentFileReaderI source = null; // alternative specification of where data
- // comes
-
- // from
+ AlignmentFileReaderI source; // alternative specification of where data
+ // comes from
AlignViewport viewport;
this.raiseGUI = raiseGUI;
}
- public void LoadFile(AlignViewport viewport, Object file,
+ /**
+ * It is critical that all these fields are set, as this instance is reused.
+ *
+ * @param source
+ * @param file
+ * @param inFile
+ * @param dataSourceType
+ * @param format
+ */
+ private void setFileFields(AlignmentFileReaderI source, File file,
+ String inFile, DataSourceType dataSourceType, FileFormatI format)
+ {
+ this.source = source;
+ this.file = inFile;
+ this.selectedFile = file;
+ this.protocol = dataSourceType;
+ this.format = format;
+ }
+
+
+ /**
+ * Uppercase LoadFile is deprecated because it does not pass byte[] data to
+ * JavaScript
+ *
+ * @param viewport
+ * @param file
+ * @param protocol
+ * @param format
+ */
+ @Deprecated
+ public void LoadFile(AlignViewport viewport, String file,
DataSourceType protocol, FileFormatI format)
{
- this.viewport = viewport;
- if (file instanceof File) {
- this.selectedFile = (File) file;
- file = selectedFile.getPath();
+ if (viewport != null)
+ {
+ this.viewport = viewport;
}
- LoadFile(file.toString(), protocol, format);
+ loadFile(file, protocol, format);
}
+ public void LoadFile(AlignViewport viewport, File file,
+ DataSourceType protocol, FileFormatI format)
+ {
+ loadFile(viewport, file, protocol, format);
+ }
+
+ /**
+ * Uppercase LoadFile is deprecated because it does not pass byte[] data to
+ * JavaScript
+ *
+ * @param file
+ * @param protocol
+ * @param format
+ */
+ @Deprecated
public void LoadFile(String file, DataSourceType protocol,
FileFormatI format)
{
+ loadFile(file, protocol, format);
+ }
+
+ /**
+ * necessary to use Object here in order to pass the file data
+ *
+ * @param viewport
+ * @param file
+ * File preferably to String
+ * @param protocol
+ * @param format
+ */
+ public void loadFile(AlignViewport viewport, File file,
+ DataSourceType protocol, FileFormatI format)
+ {
+ if (viewport != null)
+ {
+ this.viewport = viewport;
+ }
+ this.selectedFile = file;
+ loadFile(selectedFile.getPath(), protocol, format);
+ }
+
+ private void loadFile(String file, DataSourceType protocol,
+ FileFormatI format)
+ {
this.file = file;
this.protocol = protocol;
this.format = format;
}
/**
- * Load a (file, protocol) source of unknown type
- *
- * @param file
- * @param protocol
- */
- public void LoadFile(String file, DataSourceType protocol)
- {
- LoadFile(file, protocol, null);
- }
-
- /**
* Load alignment from (file, protocol) and wait till loaded
*
* @param file
* @param sourceType
* @return alignFrame constructed from file contents
*/
+ @Deprecated
public AlignFrame LoadFileWaitTillLoaded(String file,
DataSourceType sourceType)
{
* @param format
* @return alignFrame constructed from file contents
*/
+ @Deprecated
public AlignFrame LoadFileWaitTillLoaded(String file,
DataSourceType sourceType, FileFormatI format)
{
- this.file = file;
- this.protocol = sourceType;
- this.format = format;
- return _LoadFileWaitTillLoaded();
+ setFileFields(null, null, file, sourceType, format);
+ return _loadFileWaitTillLoaded();
}
/**
* Load alignment from (file, protocol) of type format and wait till loaded
*
- * @param file
+ * @param fileObject
* @param sourceType
* @param format
* @return alignFrame constructed from file contents
+ * @throws NullPointerException
+ * if {@code file} is null
*/
- public AlignFrame LoadFileWaitTillLoaded(File file,
+ public AlignFrame loadFileWaitTillLoaded(File fileObject,
DataSourceType sourceType, FileFormatI format)
{
- this.selectedFile = file;
- this.file = file.getPath();
- this.protocol = sourceType;
- this.format = format;
- return _LoadFileWaitTillLoaded();
+ setFileFields(null, fileObject, fileObject.getPath(), sourceType, format);
+ return _loadFileWaitTillLoaded();
}
/**
- * Load alignment from FileParse source of type format and wait till loaded
- *
- * @param source
- * @param format
- * @return alignFrame constructed from file contents
- */
- public AlignFrame LoadFileWaitTillLoaded(AlignmentFileReaderI source,
- FileFormatI format)
- {
- this.source = source;
-
- file = source.getInFile();
- protocol = source.getDataSourceType();
- this.format = format;
- return _LoadFileWaitTillLoaded();
- }
-
- /**
- * runs the 'run' method (in this thread), then return the alignFrame that's
- * (hopefully) been read
+ * Runs the 'run' method (in this thread), then returns the alignFrame that
+ * (hopefully) has been constructed
*
* @return
*/
- protected AlignFrame _LoadFileWaitTillLoaded()
+ private AlignFrame _loadFileWaitTillLoaded()
{
this.run();
-
return alignFrame;
}
+ /**
+ * Updates the Jalview properties file to add the last file or URL read to the
+ * tab-separated list in property RECENT_FILE or RECENT_URL respectively. The
+ * property is created if it does not already exist. The new entry is added as
+ * the first item (without duplication). If the list exceeds some maximum
+ * length (currently 10 entries), the oldest (last) entry is dropped.
+ * <p>
+ * Files read from the temporary file directory are not added to the property.
+ * <p>
+ * Property DEFAULT_FILE_FORMAT (e.g. "Fasta" etc) is also set if currently
+ * reading from file.
+ */
public void updateRecentlyOpened()
{
- Vector<String> recent = new Vector<>();
+ List<String> recent = new ArrayList<>();
if (protocol == DataSourceType.PASTE)
{
// do nothing if the file was pasted in as text... there is no filename to
// refer to it as.
return;
}
- if (file != null
- && file.indexOf(System.getProperty("java.io.tmpdir")) > -1)
+ // BH logic change here just includes ignoring file==null
+ if (file == null
+ || file.indexOf(System.getProperty("java.io.tmpdir")) > -1)
{
// ignore files loaded from the system's temporary directory
return;
}
- String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
- : "RECENT_URL";
+ String type = protocol == DataSourceType.FILE ? RECENT_FILE_PROPERTY
+ : RECENT_URL_PROPERTY;
String historyItems = Cache.getProperty(type);
- StringTokenizer st;
-
+ // BH simpler coding
if (historyItems != null)
{
- st = new StringTokenizer(historyItems, "\t");
+ String[] tokens = historyItems.split("\\t");
- while (st.hasMoreTokens())
+ for (String token : tokens)
{
- recent.addElement(st.nextToken().trim());
+ recent.add(token.trim());
}
}
recent.remove(file);
}
- StringBuffer newHistory = new StringBuffer(file);
- for (int i = 0; i < recent.size() && i < 10; i++)
+ StringBuilder newHistory = new StringBuilder(file);
+ for (int i = 0; i < recent.size() && i < MAX_HISTORY - 1; i++)
{
- newHistory.append("\t");
- newHistory.append(recent.elementAt(i));
+ newHistory.append(TAB);
+ newHistory.append(recent.get(i));
}
Cache.setProperty(type, newHistory.toString());
if (protocol == DataSourceType.FILE)
{
- Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName());
+ Cache.setProperty(DEFAULT_FILE_FORMAT_PROPERTY, format.getName());
}
}
Runtime rt = Runtime.getRuntime();
try
{
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
- Desktop.instance.startLoading(file);
+ Desktop.getInstance().startLoading(file);
}
if (format == null)
{
if (format == null)
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
System.err.println("The input file \"" + file
+ "\" has null or unidentifiable data content!");
if (!Jalview.isHeadlessMode())
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.couldnt_read_data")
+ " in " + file + "\n"
+ AppletFormatAdapter.getSupportedFormats(),
}
// TODO: cache any stream datasources as a temporary file (eg. PDBs
// retrieved via URL)
- if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+ if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
{
System.gc();
memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
// We read the data anyway - it might make sense.
}
// BH 2018 switch to File object here instead of filename
+ Platform.timeCheck(null, Platform.TIME_MARK);
alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(selectedFile == null ? file : selectedFile);
+ Platform.timeCheck("JVP loaded", Platform.TIME_MARK);
+
}
else
{
if (downloadStructureFile)
{
String structExt = format.getExtensions().split(",")[0];
- String urlLeafName = file.substring(
- file.lastIndexOf(
- System.getProperty("file.separator")),
+ int pt = file.lastIndexOf(file.indexOf('/') >= 0 ? "/"
+ : System.getProperty("file.separator"));
+ String urlLeafName = file.substring(pt,
file.lastIndexOf("."));
String tempStructureFileStr = createNamedJvTempFile(
urlLeafName, structExt);
- // BH - switching to File object here so as to hold
- // ._bytes array directly
+ // BH - switching to File object here so as to hold on to the
+ // bytes array directly
File tempFile = new File(tempStructureFileStr);
UrlDownloadClient.download(file, tempFile);
{
// register PDB entries with desktop's structure selection
// manager
- StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ Desktop.getStructureSelectionManager()
.registerPDBEntry(pdbe);
}
}
// status in Jalview 3
// TODO: define 'virtual desktop' for benefit of headless scripts
// that perform queries to find the 'current working alignment'
- Desktop.addInternalFrame(alignFrame, title,
+
+
+ Dimension dim = Platform.getDimIfEmbedded(alignFrame,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ alignFrame.setSize(dim);
+ Desktop.addInternalFrame(alignFrame, title, dim.width,
+ dim.height);
}
try
}
else
{
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
}
final String errorMessage = MessageManager.getString(
"label.couldnt_load_file") + " " + title + "\n" + error;
// TODO: refactor FileLoader to be independent of Desktop / Applet GUI
// bits ?
- if (raiseGUI && Desktop.desktop != null)
+ if (raiseGUI && Desktop.getDesktopPane() != null)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
errorMessage,
MessageManager
.getString("label.error_loading_file"),
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.problems_opening_file", new String[]
{ file }),
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"warn.out_of_memory_loading_file", new String[]
{ file }),
// memory
// after
// load
- if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+ if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
{
if (alignFrame != null)
{
}
}
// remove the visual delay indicator
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
}
}
// /SAVE THE TREES
// /////////////////////////////////
// FIND ANY ASSOCIATED TREES
- if (Desktop.desktop != null)
+ if (Desktop.getDesktopPane() != null)
{
- javax.swing.JInternalFrame[] frames = Desktop.instance
+ javax.swing.JInternalFrame[] frames = Desktop.getInstance()
.getAllFrames();
for (int t = 0; t < frames.length; t++)
if (mappings != null)
{
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ .getStructureSelectionManager(Desktop.getInstance())
.registerMappings(mappings);
}
}
{
// This must be outside the run() body as java 1.5
// will not return any value from the OptionPane to the expired thread.
- int reply = JvOptionPane.showConfirmDialog(Desktop.desktop,
+ int reply = JvOptionPane.showConfirmDialog(Desktop.getDesktopPane(),
"Automatically update suggested ids?",
"Auto replace sequence ids", JvOptionPane.YES_NO_OPTION);
String atts = gff[ATTRIBUTES_COL];
Map<String, List<String>> attributes = parseNameValuePairs(atts);
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
if (so.isA(soTerm, SequenceOntologyI.PROTEIN_MATCH))
{
sf = processProteinMatch(attributes, seq, gff, align, newseqs,
desc = target.split(" ")[0];
}
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
String type = sf.getType();
if (so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT))
{
*/
public static boolean recognises(String[] columns)
{
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
String type = columns[TYPE_COL];
if (so.isA(type, SequenceOntologyI.PROTEIN_MATCH)
|| (".".equals(columns[SOURCE_COL])
*/
package jalview.io.gff;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+
/**
* A factory class that returns a model of the Sequence Ontology. By default a
- * hard-coded subset is used (for the applet, or testing), or setInstance() can
- * be used to set full Ontology data.
+ * hard-coded subset is used (for the applet, or testing), or
+ * setSequenceOntology() can be used to set full Ontology data.
*
* @author gmcarstairs
*
*/
-public class SequenceOntologyFactory
+public class SequenceOntologyFactory implements ApplicationSingletonI
{
- private static SequenceOntologyI instance;
+ /**
+ * Answers an instance of this class for the current application context. Note
+ * that this supports running two JS 'applets' on the same page, one with the
+ * full Sequence Ontology (USE_FULL_SO = true) and one with a hard-coded
+ * subset (USE_FULL_SO = false). If this is overkill, could change this method
+ * to just return a common static instance.
+ *
+ * @return
+ */
+ private static synchronized SequenceOntologyFactory getInstance()
+ {
+ return (SequenceOntologyFactory) ApplicationSingletonProvider
+ .getInstance(SequenceOntologyFactory.class);
+ }
+
+ /**
+ * Answers the configured model of the Sequence Ontology.
+ *
+ * @return
+ */
+ public static synchronized SequenceOntologyI getSequenceOntology()
+ {
+ SequenceOntologyFactory f = getInstance();
+ return (f.sequenceOntology == null
+ ? f.sequenceOntology = new SequenceOntologyLite()
+ : f.sequenceOntology);
+ }
- public static synchronized SequenceOntologyI getInstance()
+ /**
+ * For testng only
+ *
+ * @param so
+ */
+ public static void setSequenceOntology(SequenceOntologyI so)
{
- if (instance == null)
- {
- instance = new SequenceOntologyLite();
- }
- return instance;
+ getInstance().sequenceOntology = so;
}
- public static void setInstance(SequenceOntologyI so)
+ private SequenceOntologyI sequenceOntology;
+
+ private SequenceOntologyFactory()
{
- instance = so;
+ // private singleton
}
+
}
}
bindjvvobj(mapping, sequenceMapping);
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ .getStructureSelectionManager(Desktop.getInstance())
.registerMapping(acf);
// Try to link up any conjugate database references in the two sequences
// matchConjugateDBRefs(from, to, mapping);
*/
package jalview.javascript;
-import jalview.bin.JalviewLite;
+import jalview.api.JalviewApp;
import java.net.URL;
+import java.util.Hashtable;
import java.util.Vector;
import netscape.javascript.JSObject;
public class JSFunctionExec implements Runnable
{
- public JalviewLite jvlite;
+ public JalviewApp jvlite;
- public JSFunctionExec(JalviewLite applet)
+ protected boolean debug;
+
+ public JSFunctionExec(JalviewApp applet, boolean debug)
{
jvlite = applet;
-
- jsExecQueue = jvlite.getJsExecQueue();
- jvlite.setExecutor(this);
+ this.debug = debug;
+ jsExecQueue = jvlite.getJsExecQueue(this);
}
- private Vector jsExecQueue;
+ private Vector<Runnable> jsExecQueue;
private Thread executor = null;
{
if (jsExecQueue != null)
{
- Vector<JSFunctionExec> q = null;
+ Vector<Runnable> q = null;
synchronized (jsExecQueue)
{
q = jsExecQueue;
}
if (q != null)
{
- for (JSFunctionExec jx : q)
+ for (Runnable jx : q)
{
- jx.jvlite = null;
+ ((JSFunctionExec) jx).jvlite = null;
}
q.removeAllElements();
{
if (jsExecQueue.size() > 0)
{
- Runnable r = (Runnable) jsExecQueue.elementAt(0);
+ Runnable r = jsExecQueue.elementAt(0);
jsExecQueue.removeElementAt(0);
try
{
JSObject scriptObject = null;
try
{
- scriptObject = JSObject.getWindow(jvlite);
+ scriptObject = jvlite.getJSObject();
} catch (Exception ex)
{
}
;
if (scriptObject != null)
{
- if (jvlite.debug && dbgMsg != null)
+ if (debug && dbgMsg != null)
{
System.err.println(dbgMsg);
}
// squash any malformedURLExceptions thrown by windows/safari
if (!(jex instanceof java.net.MalformedURLException))
{
- if (jvlite.debug)
+ if (debug)
{
System.err.println(jex);
}
if (jex instanceof netscape.javascript.JSException
- && jvlite.jsfallbackEnabled)
+ && jvlite.isJsfallbackEnabled())
{
jsex[0] = jex;
- if (jvlite.debug)
+ if (debug)
{
System.err.println("Falling back to javascript: url call");
}
sb.append("\"");
}
sb.append(")");
- if (jvlite.debug)
+ if (debug)
{
System.err.println(sb.toString());
}
{
if (executor == null)
{
- executor = new Thread(new JSFunctionExec(jvlite));
+ executor = new Thread(new JSFunctionExec(jvlite, debug));
executor.start();
}
synchronized (jsExecQueue)
}
}
+ public static void setJsMessageSet(String messageclass, String viewId,
+ String[] colcommands, JalviewApp app)
+ {
+ Hashtable<String, Hashtable<String, String[]>> jsmessages = app
+ .getJSMessages();
+ Hashtable<String, int[]> jshashes = app.getJSHashes();
+
+ Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
+ if (msgset == null)
+ {
+ msgset = new Hashtable<>();
+ jsmessages.put(messageclass, msgset);
+ }
+ msgset.put(viewId, colcommands);
+ int[] l = new int[colcommands.length];
+ for (int i = 0; i < colcommands.length; i++)
+ {
+ l[i] = colcommands[i].hashCode();
+ }
+ jshashes.put(messageclass + "|" + viewId, l);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
+ * java.lang.String)
+ */
+ public static String getJsMessage(String messageclass, String viewId,
+ JalviewApp app)
+ {
+ Hashtable<String, String[]> msgset = app.getJSMessages()
+ .get(messageclass);
+ if (msgset != null)
+ {
+ String[] msgs = msgset.get(viewId);
+ if (msgs != null)
+ {
+ for (int i = 0; i < msgs.length; i++)
+ {
+ if (msgs[i] != null)
+ {
+ String m = msgs[i];
+ msgs[i] = null;
+ return m;
+ }
+ }
+ }
+ }
+ return "";
+ }
+
+ public static boolean isJsMessageSetChanged(String string, String string2,
+ String[] colcommands, JalviewApp app)
+ {
+ int[] l = app.getJSHashes().get(string + "|" + string2);
+ if (l == null && colcommands != null)
+ {
+ return true;
+ }
+ for (int i = 0; i < colcommands.length; i++)
+ {
+ if (l[i] != colcommands[i].hashCode())
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ public void tidyUp()
+ {
+ stopQueue();
+ jvlite = null;
+ }
+
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$);
+ * Copyright (C); $$Year-Rel$$ 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.
+ * 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
*/
package jalview.javascript;
-import jalview.appletgui.AlignFrame;
+import jalview.api.AlignFrameI;
/**
* The following public methods may be called
* externally, eg via javascript in an HTML page.
*
- * <br><em>TODO: introduce abstract interface for jalview.appletgui.AlignFrame</em><br>
+ * <br><em>TODO: introduce abstract interface for jalview.appletgui.AlignFrameI</em><br>
*
* Most function arguments are strings, which contain serialised versions of lists.
* Lists of things are separated by a separator character - either the default or a user supplied one.
/**
* @return String list of selected sequence IDs, each terminated by the
- * 'boolean not' character (""+0x00AC) or (¬)
+ * 'boolean not' character (""+0x00AC); or (¬);
*/
public abstract String getSelectedSequences();
/**
* @param alf
- * alignframe containing selection
+ * AlignFrameI containing selection
* @return String list of selected sequence IDs, each terminated by current
* default separator sequence
*
*/
- public abstract String getSelectedSequencesFrom(AlignFrame alf);
+ public abstract String getSelectedSequencesFrom(AlignFrameI alf);
/**
* get list of selected sequence IDs separated by given separator
* @return String list of selected sequence IDs, each terminated by the given
* separator
*/
- public abstract String getSelectedSequencesFrom(AlignFrame alf,
+ public abstract String getSelectedSequencesFrom(AlignFrameI alf,
String sep);
/**
* false, blank or something else - indicate if position is an
* alignment column or unaligned sequence position
*/
- public abstract void highlightIn(AlignFrame alf, String sequenceId,
+ public abstract void highlightIn(AlignFrameI alf, String sequenceId,
String position, String alignedPosition);
/**
* @param sep
* separator between toselect fields
*/
- public abstract void selectIn(AlignFrame alf, String sequenceIds,
+ public abstract void selectIn(AlignFrameI alf, String sequenceIds,
String columns);
/**
* @param sep
* separator between toselect fields
*/
- public abstract void selectIn(AlignFrame alf, String sequenceIds,
+ public abstract void selectIn(AlignFrameI alf, String sequenceIds,
String columns, String sep);
/**
- * get sequences selected in current alignFrame and return their alignment in
+ * get sequences selected in current AlignFrameI and return their alignment in
* format 'format' either with or without suffix
*
* @param alf
* @return selected sequences as flat file or empty string if there was no
* current selection
*/
- public abstract String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
+ public abstract String getSelectedSequencesAsAlignmentFrom(
+ AlignFrameI alf,
String format, String suffix);
/**
* @param alf
* @return
*/
- public abstract String getAlignmentOrderFrom(AlignFrame alf);
+ public abstract String getAlignmentOrderFrom(AlignFrameI alf);
/**
* get a sep separated list of sequence IDs reflecting the order of the
* - separator to use
* @return
*/
- public abstract String getAlignmentOrderFrom(AlignFrame alf, String sep);
+ public abstract String getAlignmentOrderFrom(AlignFrameI alf,
+ String sep);
/**
* re-order the current alignment using the given list of sequence IDs
* @return 'true' if alignment was actually reordered. empty string if
* alignment did not contain sequences.
*/
- public abstract String orderBy(String order, String undoName, String sep);
+ public abstract String orderBy(String order, String undoName,
+ String sep);
/**
* re-order the given alignment using the given list of sequence IDs separated
* @return 'true' if alignment was actually reordered. empty string if
* alignment did not contain sequences.
*/
- public abstract String orderAlignmentBy(AlignFrame alf, String order,
+ public abstract String orderAlignmentBy(AlignFrameI alf, String order,
String undoName, String sep);
/**
* get alignment as format (format names FASTA, BLC, CLUSTAL, MSF, PILEUP,
- * PFAM - see jalview.io.AppletFormatAdapter for full list)
+ * PFAM - see jalview.io.AppletFormatAdapter for full list);
*
* @param format
* @return
* @param format
* @return
*/
- public abstract String getAlignmentFrom(AlignFrame alf, String format);
+ public abstract String getAlignmentFrom(AlignFrameI alf, String format);
/**
* get alignment as format with jalview start-end sequence suffix appended
* @param suffix
* @return
*/
- public abstract String getAlignmentFrom(AlignFrame alf, String format,
+ public abstract String getAlignmentFrom(AlignFrameI alf, String format,
String suffix);
/**
* @param alf
* @param annotation
*/
- public abstract void loadAnnotationFrom(AlignFrame alf,
+ public abstract void loadAnnotationFrom(AlignFrameI alf,
String annotation);
/**
* parse the given string as a jalview feature or GFF annotation file and
- * optionally enable feature display on the current alignFrame
+ * optionally enable feature display on the current AlignFrameI
*
* @param features
* - gff or features file
/**
* parse the given string as a jalview feature or GFF annotation file and
- * optionally enable feature display on the given alignFrame.
+ * optionally enable feature display on the given AlignFrameI.
*
* @param alf
* @param features
* be parsed from the string.
* @return true if data parsed as features
*/
- public abstract boolean loadFeaturesFrom(AlignFrame alf, String features,
+ public abstract boolean loadFeaturesFrom(AlignFrameI alf, String features,
boolean autoenabledisplay);
/**
- * get the sequence features in the given format (Jalview or GFF)
+ * get the sequence features in the given format (Jalview or GFF);
*
* @param format
* @return
public abstract String getFeatures(String format);
/**
- * get the sequence features in alf in the given format (Jalview or GFF)
+ * get the sequence features in alf in the given format (Jalview or GFF);
*
* @param alf
* @param format
* @return
*/
- public abstract String getFeaturesFrom(AlignFrame alf, String format);
+ public abstract String getFeaturesFrom(AlignFrameI alf, String format);
/**
* get current alignment's annotation as an annotation file
* @param alf
* @return
*/
- public abstract String getAnnotationFrom(AlignFrame alf);
+ public abstract String getAnnotationFrom(AlignFrameI alf);
/**
- * create a new view and return the alignFrame instance
+ * create a new view and return the AlignFrameI instance
*
* @return
*/
- public abstract AlignFrame newView();
+ public abstract AlignFrameI newView();
/**
- * create a new view named name and return the alignFrame instance
+ * create a new view named name and return the AlignFrameI instance
*
* @param name
* @return
*/
- public abstract AlignFrame newView(String name);
+ public abstract AlignFrameI newView(String name);
/**
- * create a new view on alf and return the alignFrame instance
+ * create a new view on alf and return the AlignFrameI instance
*
* @param alf
* @return
*/
- public abstract AlignFrame newViewFrom(AlignFrame alf);
+ public abstract AlignFrameI newViewFrom(AlignFrameI alf);
/**
* create a new view named name on alf
* @param name
* @return
*/
- public abstract AlignFrame newViewFrom(AlignFrame alf, String name);
+ public abstract AlignFrameI newViewFrom(AlignFrameI alf, String name);
/**
*
* window title
* @return null or new alignment frame
*/
- public abstract AlignFrame loadAlignment(String text, String title);
+ public abstract AlignFrameI loadAlignment(String text, String title);
/**
* register a javascript function to handle any alignment mouseover events
*
* @param listener
* name of javascript function (called with arguments
- * [jalview.appletgui.AlignFrame,String(sequence id),String(column in
- * alignment), String(position in sequence)]
+ * [jalview.appletgui.AlignFrameI,String(sequence id);,String(column
+ * in alignment);, String(position in sequence);]
*/
public abstract void setMouseoverListener(String listener);
* register a javascript function to handle mouseover events
*
* @param af
- * (null or specific alignframe for which events are to be listened
- * for)
+ * (null or specific AlignFrameI for which events are to be listened
+ * for);
* @param listener
* name of javascript function
*/
- public abstract void setMouseoverListener(AlignFrame af, String listener);
+ public abstract void setMouseoverListener(AlignFrameI af,
+ String listener);
/**
* register a javascript function to handle any alignment selection events.
*
* @param listener
* name of javascript function (called with arguments
- * [jalview.appletgui.AlignFrame, String(sequence set id),
- * String(separator separated list of sequences which were selected),
- * String(separator separated list of column ranges (i.e. single
- * number or hyphenated range) that were selected)]
+ * [jalview.appletgui.AlignFrameI, String(sequence set id);,
+ * String(separator separated list of sequences which were
+ * selected);, String(separator separated list of column ranges (i.e.
+ * single number or hyphenated range); that were selected);]
*/
public abstract void setSelectionListener(String listener);
- public abstract void setSelectionListener(AlignFrame af, String listener);
+ public abstract void setSelectionListener(AlignFrameI af,
+ String listener);
/**
* register a javascript function to handle events normally routed to a Jmol
*
* @param listener
* - javascript function (arguments are variable, see
- * jalview.javascript.MouseOverStructureListener for full details)
+ * jalview.javascript.MouseOverStructureListener for full details);
* @param modelSet
* - separator separated list of PDB file URIs that this viewer is
* handling. These files must be in the same order they appear in
- * Jmol (e.g. first one is frame 1, second is frame 2, etc).
+ * Jmol (e.g. first one is frame 1, second is frame 2, etc);.
* @see jalview.javascript.MouseOverStructureListener
*/
public abstract void setStructureListener(String listener,
/**
* remove any callback using the given listener function and associated with
- * the given alignFrame (or null for all callbacks)
+ * the given AlignFrameI (or null for all callbacks);
*
* @param af
- * (may be null)
+ * (may be null);
* @param listener
- * (may be null)
+ * (may be null);
*/
- public abstract void removeJavascriptListener(AlignFrame af,
+ public abstract void removeJavascriptListener(AlignFrameI af,
String listener);
/**
String pdbfile);
/**
- * bind a pdb file to a sequence in the given alignFrame.
+ * bind a pdb file to a sequence in the given AlignFrameI.
*
* @param alFrame
- * - null or specific alignFrame. This specifies the dataset that
+ * - null or specific AlignFrameI. This specifies the dataset that
* will be searched for a seuqence called sequenceId
* @param sequenceId
* - sequenceId within the dataset.
* structure for indicating when PDB parsing or sequenceId location
* fails.
*/
- public abstract boolean addPdbFile(AlignFrame alFrame, String sequenceId,
+ public abstract boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
String pdbEntryString, String pdbFile);
/**
* @param topRow
* @param leftHandColumn
*/
- public abstract void scrollViewToIn(AlignFrame alf, String topRow,
+ public abstract void scrollViewToIn(AlignFrameI alf, String topRow,
String leftHandColumn);
/**
* @param alf
* @param topRow
*/
- public abstract void scrollViewToRowIn(AlignFrame alf, String topRow);
+ public abstract void scrollViewToRowIn(AlignFrameI alf, String topRow);
/**
* adjust horizontal scroll to make the given column the left one in the given
* @param alf
* @param leftHandColumn
*/
- public abstract void scrollViewToColumnIn(AlignFrame alf,
+ public abstract void scrollViewToColumnIn(AlignFrameI alf,
String leftHandColumn);
/**
*
* @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroups()
+ * @see jalview.appletgui.AlignFrameI#getFeatureGroups();
*/
public abstract String getFeatureGroups();
/**
* @param alf
- * alignframe to get feature groups on
+ * AlignFrameI to get feature groups on
* @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroups()
+ * @see jalview.appletgui.AlignFrameI#getFeatureGroups();
*/
- public abstract String getFeatureGroupsOn(AlignFrame alf);
+ public abstract String getFeatureGroupsOn(AlignFrameI alf);
/**
* @param visible
* @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
+ * @see jalview.appletgui.AlignFrameI#getFeatureGroupsOfState(boolean);
*/
public abstract String getFeatureGroupsOfState(boolean visible);
* align frame to get groups of state visible
* @param visible
* @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
+ * @see jalview.appletgui.AlignFrameI#getFeatureGroupsOfState(boolean);
*/
- public abstract String getFeatureGroupsOfStateOn(AlignFrame alf,
+ public abstract String getFeatureGroupsOfStateOn(AlignFrameI alf,
boolean visible);
/**
* tab separated list of group names
* @param state
* true or false
- * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
- * boolean)
+ * @see jalview.appletgui.AlignFrameI#setFeatureGroupState(java.lang.String[],
+ * boolean);
*/
- public abstract void setFeatureGroupStateOn(AlignFrame alf, String groups,
+ public abstract void setFeatureGroupStateOn(AlignFrameI alf,
+ String groups,
boolean state);
public abstract void setFeatureGroupState(String groups, boolean state);
*/
public abstract String getJsMessage(String messageclass, String viewId);
+ /// in http://www.jalview.org/examples/jalviewLiteJs.html but missing here
+
+ // get selected sequences as alignment as format with or without start-end
+ // suffix
+ public String getSelectedSequencesAsAlignment(String format,
+ boolean suffix);
+
+ // get selected sequences as alignment from given view as format with or
+ // without start-end suffix
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+ String format, boolean suffix);
+
+ public String arrayToSeparatorList(String[] array);
+
+ // get a string array from a list
+ public String[] separatorListToArray(String list);
+
+ // debug flag - controls output to standard out
+ public static boolean debug = false;
+
}
*/
package jalview.javascript;
+import jalview.api.JalviewApp;
import jalview.appletgui.AlignFrame;
-import jalview.bin.JalviewLite;
import jalview.datamodel.SequenceI;
import jalview.structure.VamsasListener;
import jalview.structure.VamsasSource;
// + seq + " at " + index);
last = seq;
i = index;
- AlignFrame src = null;
+ Object alignFrame = jvlite.getFrameForSource(source);
try
{
- if (source != null)
- {
- if (source instanceof jalview.appletgui.AlignViewport
- && ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame.viewport == source)
- {
- // should be valid if it just generated an event!
- src = ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame;
-
- }
- // TODO: ensure that if '_af' is specified along with a handler
- // function, then only events from that alignFrame are sent to that
- // function
- }
executeJavascriptFunction(_listener,
new Object[]
- { src, seq.getDisplayId(false), "" + (1 + i),
+ { alignFrame, seq.getDisplayId(false), "" + (1 + i),
"" + seq.findPosition(i) });
} catch (Exception ex)
{
}
}
- public MouseOverListener(JalviewLite applet, AlignFrame af,
- String listener)
+ public MouseOverListener(JalviewApp applet, AlignFrame af,
+ String listener, boolean debug)
{
- super(applet);
+ super(applet, debug);
_af = af;
_listener = listener;
}
package jalview.jbgui;
import jalview.api.AlignmentViewPanel;
+import jalview.bin.Jalview;
import jalview.io.FileFormatException;
import jalview.util.MessageManager;
import jalview.util.Platform;
import java.awt.FlowLayout;
+import java.awt.Toolkit;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.JMenuItem;
/**
- * DOCUMENT ME!
+ * abstract class super to jalview.gui.Desktop
*
- * @author $author$
- * @version $Revision$
*/
@SuppressWarnings("serial")
-public class GDesktop extends JFrame
+// BH made abstract
+public abstract class GDesktop extends JFrame
{
- protected static JMenu windowMenu = new JMenu();
+ protected JMenu windowMenu = new JMenu(); // BH 2019.05.07 was static
JMenuBar desktopMenubar = new JMenuBar();
JMenu HelpMenu = new JMenu();
+ protected JMenu VamsasMenu = new JMenu();
+
+ protected JMenu VamsasStMenu = new JMenu();
+
JMenuItem inputLocalFileMenuItem = new JMenuItem();
JMenuItem inputURLMenuItem = new JMenuItem();
JMenu inputMenu = new JMenu();
+ // in JalviewJS
+ protected JMenuItem vamsasStart = new JMenuItem();
+
+ protected JMenuItem vamsasImport = new JMenuItem();
+
+ protected JMenuItem vamsasSave = new JMenuItem();
+
+ protected JMenuItem vamsasStop = new JMenuItem();
+
JMenuItem inputSequence = new JMenuItem();
JMenuItem closeAll = new JMenuItem();
protected JCheckBoxMenuItem showConsole = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem showNews = new JCheckBoxMenuItem();
+ // BH public for Runnable
+ public JCheckBoxMenuItem showNews = new JCheckBoxMenuItem();
protected JMenuItem snapShotWindow = new JMenuItem();
*/
public GDesktop()
{
- super();
try
{
jbInit();
// but here we want just not a Mac, period, right?
FileMenu.setMnemonic('F');
inputLocalFileMenuItem.setMnemonic('L');
+ VamsasMenu.setMnemonic('V');
inputURLMenuItem.setMnemonic('U');
inputTextboxMenuItem.setMnemonic('C');
quit.setMnemonic('Q');
*/
private void jbInit() throws Exception
{
- setName("jalview-desktop");
+ setName(Jalview.getAppID("desktop"));
FileMenu.setText(MessageManager.getString("action.file"));
HelpMenu.setText(MessageManager.getString("action.help"));
+ VamsasMenu.setText("Vamsas");
+ VamsasMenu.setToolTipText(MessageManager
+ .getString("label.share_data_vamsas_applications"));
+ VamsasStMenu.setText(MessageManager.getString("label.connect_to"));
+ VamsasStMenu.setToolTipText(
+ MessageManager.getString("label.join_existing_vamsas_session"));
inputLocalFileMenuItem
.setText(MessageManager.getString("label.load_tree_from_file"));
inputLocalFileMenuItem.setAccelerator(
javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_O,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(),
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(),
false));
inputLocalFileMenuItem
.addActionListener(new java.awt.event.ActionListener()
}
});
inputMenu.setText(MessageManager.getString("label.input_alignment"));
+ vamsasStart
+ .setText(MessageManager.getString("label.new_vamsas_session"));
+ vamsasStart.setVisible(false);
+ vamsasStart.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ vamsasStart_actionPerformed(e);
+ }
+ });
+ vamsasImport.setText(
+ MessageManager.getString("action.load_vamsas_session"));
+ vamsasImport.setVisible(false);
+ vamsasImport.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ vamsasImport_actionPerformed(e);
+ }
+ });
+ vamsasSave.setText(
+ MessageManager.getString("action.save_vamsas_session"));
+ vamsasSave.setVisible(false);
+ vamsasSave.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ vamsasSave_actionPerformed(e);
+ }
+ });
inputSequence
.setText(MessageManager.getString("action.fetch_sequences"));
inputSequence.addActionListener(new ActionListener()
inputSequence_actionPerformed(e);
}
});
+ vamsasStop
+ .setText(MessageManager.getString("label.stop_vamsas_session"));
+ vamsasStop.setVisible(false);
+ vamsasStop.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ vamsasStop_actionPerformed(e);
+ }
+ });
closeAll.setText(MessageManager.getString("action.close_all"));
closeAll.addActionListener(new ActionListener()
{
}
});
- Float specversion = Platform.isJS() ? Float.valueOf(8)
- : Float.parseFloat(
- System.getProperty("java.specification.version"));
-
desktopMenubar.add(FileMenu);
desktopMenubar.add(toolsMenu);
+ VamsasMenu.setVisible(false);
+ desktopMenubar.add(VamsasMenu);
desktopMenubar.add(HelpMenu);
desktopMenubar.add(windowMenu);
FileMenu.add(inputMenu);
FileMenu.add(inputSequence);
FileMenu.addSeparator();
- //FileMenu.add(saveState);
+ FileMenu.add(saveState);
FileMenu.add(saveAsState);
FileMenu.add(loadState);
FileMenu.addSeparator();
FileMenu.add(quit);
HelpMenu.add(aboutMenuItem);
HelpMenu.add(documentationMenuItem);
- if (!Platform.isAMacAndNotJS() || specversion < 11)
- {
- toolsMenu.add(preferences);
- }
+ VamsasMenu.add(VamsasStMenu);
+ VamsasStMenu.setVisible(false);
+ VamsasMenu.add(vamsasStart);
+ VamsasMenu.add(vamsasImport);
+ VamsasMenu.add(vamsasSave);
+ VamsasMenu.add(vamsasStop);
+ toolsMenu.add(preferences);
if (!Platform.isJS())
{
toolsMenu.add(showMemusage);
toolsMenu.add(showConsole);
+ }
+ if (!Platform.isJS())
+ {
toolsMenu.add(showNews);
toolsMenu.add(garbageCollect);
toolsMenu.add(groovyShell);
*/
protected void quit()
{
- //System.out.println("********** GDesktop.quit()");
}
/**
return true;
}
- JvOptionPane.showInternalMessageDialog(jalview.gui.Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(jalview.gui.Desktop.getDesktopPane(),
MessageManager.getString("warn.url_must_contain"),
MessageManager.getString("label.invalid_url"),
JvOptionPane.WARNING_MESSAGE);
public void notifyDuplicate()
{
- JvOptionPane.showInternalMessageDialog(jalview.gui.Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(jalview.gui.Desktop.getDesktopPane(),
MessageManager.getString("warn.name_cannot_be_duplicate"),
MessageManager.getString("label.invalid_name"),
JvOptionPane.WARNING_MESSAGE);
* only view *should* be coped with sensibly.
*/
// This must have been loaded, is it still visible?
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
String matchedFile = null;
for (int f = frames.length - 1; f > -1; f--)
{
{
// FIND ANY ASSOCIATED TREES
// NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
- if (Desktop.desktop != null)
+ if (Desktop.getDesktopPane() != null)
{
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
for (int t = 0; t < frames.length; t++)
{
/*
* save PCA viewers
*/
- if (!storeDS && Desktop.desktop != null)
+ if (!storeDS && Desktop.getDesktopPane() != null)
{
- for (JInternalFrame frame : Desktop.desktop.getAllFrames())
+ for (JInternalFrame frame : Desktop.getDesktopPane().getAllFrames())
{
if (frame instanceof PCAPanel)
{
final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
boolean storeDataset)
{
- if (Desktop.desktop == null)
+ if (Desktop.getDesktopPane() == null)
{
return;
}
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
for (int f = frames.length - 1; f > -1; f--)
{
if (frames[f] instanceof AppVarna)
if (calcIdParam.getVersion().equals("1.0"))
{
final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
- Jws2Instance service = Jws2Discoverer.getDiscoverer()
+ Jws2Instance service = Jws2Discoverer.getInstance()
.getPreferredServiceFor(calcIds);
if (service != null)
{
{
// used to attempt to parse as V1 castor-generated xml
}
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
}
if (af != null)
{
*/
for (AlignFrame fr : gatherToThisFrame.values())
{
- Desktop.instance.gatherViews(fr);
+ Desktop.getInstance().gatherViews(fr);
}
restoreSplitFrames();
if (ds.getCodonFrames() != null)
{
StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ .getStructureSelectionManager(Desktop.getInstance())
.registerMappings(ds.getCodonFrames());
}
}
reportErrors();
}
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
}
return af;
*/
for (SplitFrame sf : gatherTo)
{
- Desktop.instance.gatherViews(sf);
+ Desktop.getInstance().gatherViews(sf);
}
splitFrameCandidates.clear();
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
finalErrorMessage,
"Error " + (saving ? "saving" : "loading")
+ " Jalview file",
entry.setProperty(prop.getName(), prop.getValue());
}
StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ .getStructureSelectionManager(Desktop.getInstance())
.registerPDBEntry(entry);
// adds PDBEntry to datasequence's set (since Jalview 2.10)
if (al.getSequenceAt(i).getDatasetSequence() != null)
int height = safeInt(structureState.getHeight());
// Probably don't need to do this anymore...
- // Desktop.desktop.getComponentAt(x, y);
+ // Desktop.getDesktopPane().getComponentAt(x, y);
// TODO: NOW: check that this recovers the PDB file correctly.
String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
pdbid.getFile());
{
try
{
- frames = Desktop.desktop.getAllFrames();
+ frames = Desktop.getDesktopPane().getAllFrames();
} catch (ArrayIndexOutOfBoundsException e)
{
// occasional No such child exceptions are thrown here...
import jalview.analysis.AlignSeq;
import jalview.api.StructureSelectionManagerProvider;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.OrderCommand;
import mc_view.PDBChain;
import mc_view.PDBfile;
-public class StructureSelectionManager
+public class StructureSelectionManager implements ApplicationSingletonI
{
public final static String NEWLINE = System.lineSeparator();
- static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
-
private List<StructureMapping> mappings = new ArrayList<>();
private boolean processSecondaryStructure = false;
private List<SelectionListener> sel_listeners = new ArrayList<>();
+ /*
+ * instances of this class scoped by some context class
+ */
+ private IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> selectionManagers;
+
+ /**
+ * Answers an instance of this class for the current application (Java or JS
+ * 'applet') scope
+ *
+ * @return
+ */
+ private static StructureSelectionManager getInstance()
+ {
+ return (StructureSelectionManager) ApplicationSingletonProvider
+ .getInstance(StructureSelectionManager.class);
+ }
+
+ /**
+ * Answers an instance of this class for the current application (Java or JS
+ * 'applet') scope, and scoped to the specified context
+ *
+ * @param context
+ * @return
+ */
+ public static StructureSelectionManager getStructureSelectionManager(
+ StructureSelectionManagerProvider context)
+ {
+ return getInstance().getInstanceForContext(context);
+ }
+
+ /**
+ * Answers an instance of this class scoped to the given context. The instance
+ * is created on the first request for the context, thereafter the same
+ * instance is returned. Note that the context may be null (this is the case
+ * when running headless without a Desktop).
+ *
+ * @param context
+ * @return
+ */
+ StructureSelectionManager getInstanceForContext(
+ StructureSelectionManagerProvider context)
+ {
+ StructureSelectionManager instance = selectionManagers.get(context);
+ if (instance == null)
+ {
+ instance = new StructureSelectionManager();
+ selectionManagers.put(context, instance);
+ }
+ return instance;
+ }
+
+ /**
+ * Removes the instance associated with this provider
+ *
+ * @param provider
+ */
+
+ public static void release(StructureSelectionManagerProvider provider)
+ {
+ getInstance().selectionManagers.remove(provider);
+ }
+
+ /**
+ * Private constructor as all 'singleton' instances are managed here or by
+ * ApplicationSingletonProvider
+ */
+ private StructureSelectionManager()
+ {
+ selectionManagers = new IdentityHashMap<>();
+ }
+
/**
* @return true if will try to use external services for processing secondary
* structure
|| pdbIdFileName.containsKey(idOrFile);
}
- private static StructureSelectionManager nullProvider = null;
-
- public static StructureSelectionManager getStructureSelectionManager(
- StructureSelectionManagerProvider context)
- {
- if (context == null)
- {
- if (nullProvider == null)
- {
- if (instances != null)
- {
- throw new Error(MessageManager.getString(
- "error.implementation_error_structure_selection_manager_null"),
- new NullPointerException(MessageManager
- .getString("exception.ssm_context_is_null")));
- }
- else
- {
- nullProvider = new StructureSelectionManager();
- }
- return nullProvider;
- }
- }
- if (instances == null)
- {
- instances = new java.util.IdentityHashMap<>();
- }
- StructureSelectionManager instance = instances.get(context);
- if (instance == null)
- {
- if (nullProvider != null)
- {
- instance = nullProvider;
- }
- else
- {
- instance = new StructureSelectionManager();
- }
- instances.put(context, instance);
- }
- return instance;
- }
-
/**
* flag controlling whether SeqMappings are relayed from received sequence
* mouse over events to other sequences
return relaySeqMappings;
}
- Vector listeners = new Vector();
+ Vector<Object> listeners = new Vector<>();
/**
* register a listener for alignment sequence mouseover events
* Import structure data and register a structure mapping for broadcasting
* colouring, mouseovers and selection events (convenience wrapper).
*
+ * This is the standard entry point.
+ *
* @param sequence
* - one or more sequences to be mapped to pdbFile
* @param targetChains
* broadcasting colouring, mouseovers and selection events (convenience
* wrapper).
*
+ *
+ *
* @param forStructureView
- * when true, record the mapping for use in mouseOvers
+ * when true (testng only), record the mapping for use in mouseOvers
+ * (testng only)
* @param sequence
* - one or more sequences to be mapped to pdbFile
* @param targetChains
* mapping operation
* @return null or the structure data parsed as a pdb file
*/
- synchronized public StructureFile computeMapping(
+ synchronized private StructureFile computeMapping(
boolean forStructureView, SequenceI[] sequenceArray,
String[] targetChainIds, String pdbFile, DataSourceType sourceType,
IProgressIndicator progress)
{
ds = ds.getDatasetSequence();
}
- ;
if (ds.getAnnotation() != null)
{
for (AlignmentAnnotation ala : ds.getAnnotation())
{
slis.viewPosition(startRes, endRes, startSeq, endSeq, source);
}
- ;
- }
- }
- }
-
- /**
- * release all references associated with this manager provider
- *
- * @param jalviewLite
- */
- public static void release(StructureSelectionManagerProvider jalviewLite)
- {
- // synchronized (instances)
- {
- if (instances == null)
- {
- return;
- }
- StructureSelectionManager mnger = (instances.get(jalviewLite));
- if (mnger != null)
- {
- instances.remove(jalviewLite);
- try
- {
- /* bsoares 2019-03-20 finalize deprecated, no apparent external
- * resources to close
- */
- // mnger.finalize();
- } catch (Throwable x)
- {
- }
}
}
}
-
+
public void registerPDBEntry(PDBEntry pdbentry)
{
if (pdbentry.getFile() != null
/**
*
* @return true if we are running in non-interactive no UI mode
+ * based on System.getProperty("java.awt.headless")
*/
public static boolean isHeadless()
{
return f.toString();
}
+ private static float javaVersion;
+
+ public static float getJavaVersion()
+ {
+ if (javaVersion == 0)
+ {
+ try
+ {
+ return javaVersion = Float.parseFloat(
+ System.getProperty("java.specification.version"));
+ } catch (Exception e)
+ {
+ javaVersion = 1.8f;
+ }
+ }
+ return javaVersion;
+ }
+
}
package jalview.util;
+import java.awt.Toolkit;
import java.awt.event.MouseEvent;
+/**
+ * retrieve KeyEvent masks for Java 8 or Java 11+
+ *
+ * @author hansonr
+ *
+ */
public class ShortcutKeyMaskExWrapper
{
-
- private static final Float specversion;
-
- private static final float modern;
-
public static final int SHIFT_DOWN_MASK;
public static final int ALT_DOWN_MASK;
- private static final ShortcutKeyMaskExWrapperI wrapper;
+ public static final int SHORTCUT_MASK;
static
{
- specversion = Platform.isJS() ? Float.valueOf(8)
- : Float.parseFloat(
- System.getProperty("java.specification.version"));
- modern = 11;
-
- if (specversion >= modern)
+ float specversion = Platform.getJavaVersion();
+ String method;
+ // BH technically, these are not masks; they are bits.
+ if (specversion >= 11)
{
- wrapper = new jalview.util.ShortcutKeyMaskExWrapper11();
- SHIFT_DOWN_MASK = jalview.util.ShortcutKeyMaskExWrapper11.SHIFT_DOWN_MASK;
- ALT_DOWN_MASK = jalview.util.ShortcutKeyMaskExWrapper11.ALT_DOWN_MASK;
+ SHIFT_DOWN_MASK = 0x040; // KeyEvent.SHIFT_DOWN_MASK;
+ ALT_DOWN_MASK = 0x200; // KeyEvent.ALT_DOWN_MASK;
+ method = "getMenuShortcutKeyMaskEx";
}
else
{
- wrapper = new jalview.util.ShortcutKeyMaskExWrapper8();
- SHIFT_DOWN_MASK = jalview.util.ShortcutKeyMaskExWrapper8.SHIFT_DOWN_MASK;
- ALT_DOWN_MASK = jalview.util.ShortcutKeyMaskExWrapper8.ALT_DOWN_MASK;
+ SHIFT_DOWN_MASK = 0x01; // KeyEvent.SHIFT_MASK;
+ ALT_DOWN_MASK = 0x08; // KeyEvent.ALT_MASK;
+ method = "getMenuShortcutKeyMask";
}
+
+ int mask = 0;
+ try
+ {
+ // Just use reflection -- doesn't matter what version is running.
+ Toolkit tk = Toolkit.getDefaultToolkit();
+ mask = (int) (tk.getClass().getMethod(method, new Class<?>[0])
+ .invoke(tk, new Object[0]));
+ } catch (Exception e)
+ {
+ System.out.println("Shortcut exception: " + e);
+ }
+
+ SHORTCUT_MASK = mask;
}
+ // BH Q: Why not just use the public static field?
public static int getMenuShortcutKeyMaskEx()
{
- return wrapper.getMenuShortcutKeyMaskEx();
+ return SHORTCUT_MASK;
}
+ // BH Q: Why is this here?
public static int getModifiersEx(MouseEvent e)
{
- return wrapper.getModifiersEx(e);
+ return e.getModifiersEx();
}
}
* {@code "a=b;c"}.
*
* @param s
+ * @return
+ */
+ public static boolean isHexString(String s)
+ {
+ int j = s.length();
+ if (j == 0)
+ {
+ return false;
+ }
+ for (int i = 0; i < j; i++)
+ {
+ int c = s.charAt(i);
+ if (!(c >= '0' && c <= '9') && !(c >= 'a' && c <= 'f')
+ && !(c >= 'A' && c <= 'F'))
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+ /**
+ * Answers the input string with any occurrences of the specified (unencoded)
+ * characters replaced by their URL decoding.
+ * <p>
+ * Example: {@code urlDecode("a%3Db%3Bc", "-;=,")} should answer
+ * {@code "a=b;c"}.
+ *
+ * @param s
* @param encodable
* @return
*/
}
/**
- * Does a lazy lookup of the url encoding of the given character, saving the
- * value for repeat lookups
- *
- * @param c
- * @return
- */
- private static String getUrlEncoding(char c)
- {
- if (c < 0 || c >= urlEncodings.length)
- {
- return String.valueOf(c);
- }
+ * Does a lazy lookup of the url encoding of the given character, saving the
+ * value for repeat lookups
+ *
+ * @param c
+ * @return
+ */
+ private static String getUrlEncoding(char c)
+ {
+ if (c < 0 || c >= urlEncodings.length)
+ {
+ return String.valueOf(c);
+ }
+
+ String enc = urlEncodings[c];
+ if (enc == null)
+ {
+ try
+ {
+ enc = urlEncodings[c] = URLEncoder.encode(String.valueOf(c),
+ "UTF-8");
+ } catch (UnsupportedEncodingException e)
+ {
+ enc = urlEncodings[c] = String.valueOf(c);
+ }
+ }
+ return enc;
+ }
- String enc = urlEncodings[c];
- if (enc == null)
- {
- try
- {
- enc = urlEncodings[c] = URLEncoder.encode(String.valueOf(c),
- "UTF-8");
- } catch (UnsupportedEncodingException e)
- {
- enc = urlEncodings[c] = String.valueOf(c);
- }
- }
- return enc;
- }
+
}
protected ColumnSelection colSel = new ColumnSelection();
- public boolean autoCalculateConsensus = true;
+ protected boolean autoCalculateConsensusAndConservation = true;
+
+ public boolean getAutoCalculateConsensusAndConservation()
+ { // BH 2019.07.24
+ return autoCalculateConsensusAndConservation;
+ }
+
+ public void setAutoCalculateConsensusAndConservation(boolean b)
+ {
+ autoCalculateConsensusAndConservation = b;
+ }
protected boolean autoCalculateStrucConsensus = true;
+ public boolean getAutoCalculateStrucConsensus()
+ { // BH 2019.07.24
+ return autoCalculateStrucConsensus;
+ }
+
+ public void setAutoCalculateStrucConsensus(boolean b)
+ {
+ autoCalculateStrucConsensus = b;
+ }
+
protected boolean ignoreGapsInConsensusCalculation = false;
protected ResidueShaderI residueShading = new ResidueShader();
// see note in mantis : issue number 8585
if (alignment.isNucleotide()
|| (conservation == null && quality == null)
- || !autoCalculateConsensus)
+ || !autoCalculateConsensusAndConservation)
{
return;
}
public void updateConsensus(final AlignmentViewPanel ap)
{
// see note in mantis : issue number 8585
- if (consensus == null || !autoCalculateConsensus)
+ if (consensus == null || !autoCalculateConsensusAndConservation)
{
return;
}
public void setSequenceSetId(String newid)
{
+ // // BH 2020.04.07 do we need to do this if it is the same?
+ // // (Jalview project files)
+ // if (newid.equals(sequenceSetID))
+ // {
+ // return;
+ // }
+
if (sequenceSetID != null)
{
System.err.println(
{
alignment.padGaps();
}
- if (autoCalculateConsensus)
+ if (autoCalculateConsensusAndConservation)
{
updateConsensus(ap);
}
- if (hconsensus != null && autoCalculateConsensus)
+ if (hconsensus != null && autoCalculateConsensusAndConservation)
{
updateConservation(ap);
}
visibleTypes);
/*
- * include features unless they are hidden (have no colour), based on
- * feature group visibility, or a filter or colour threshold
+ * include features unless their feature group is not displayed, or
+ * they are hidden (have no colour) based on a filter or colour threshold
*/
+
+ // BH! check -- !featureGroupNotShown(sf) is from applet branch.
for (SequenceFeature sf : features)
{
- if (getColour(sf) != null)
+ if (!featureGroupNotShown(sf) && getColour(sf) != null)
{
result.add(sf);
}
*/
public void filterFeaturesForDisplay(List<SequenceFeature> features)
{
+// BH! check -- what was the problem here? How is JalviewJS's IntervalStore different from
+ // other IntervalStore?
/*
* fudge: JalviewJS's IntervalStore lacks the sort method called :-(
*/
/**
* Answers the colour for the feature, or null if the feature is excluded by
* feature group visibility, by filters, or by colour threshold settings. This
- * method does not take feature type visibility into account.
+ * method does not take feature visibility into account.
*
* @param sf
* @param fc
import jalview.gui.FeatureSettings;
import jalview.gui.IProgressIndicator;
import jalview.gui.OOMWarning;
+import jalview.gui.Preferences;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.ws.seqfetcher.DbSourceProxy;
}
this.dataset = ds;
// TODO Jalview 2.5 lots of this code should be in the gui package!
- sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton();
+ sfetcher = SequenceFetcher.getInstance();
// set default behaviour for transferring excess sequence data to the
// dataset
trimDsSeqs = Cache.getDefault(TRIM_RETRIEVED_SEQUENCES, true);
}
try
{
- if (Cache.getDefault("DBREFFETCH_USEPICR", false))
+ if (Cache.getDefault(Preferences.DBREFFETCH_USEPICR, false))
{
picrClient = new AccessionMapperServiceLocator()
.getAccessionMapperPort();
*/
package jalview.ws;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+import jalview.datamodel.DBRefSource;
import jalview.ext.ensembl.EnsemblGene;
-import jalview.ws.dbsources.EmblCdsSource;
-import jalview.ws.dbsources.EmblSource;
-import jalview.ws.dbsources.Pdb;
-import jalview.ws.dbsources.PfamFull;
-import jalview.ws.dbsources.PfamSeed;
-import jalview.ws.dbsources.RfamSeed;
import jalview.ws.dbsources.Uniprot;
import jalview.ws.seqfetcher.ASequenceFetcher;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.List;
/**
- * This implements the run-time discovery of sequence database clients.
+ * Thread safe construction of database proxies. This implements the run-time
+ * discovery of sequence database clients.
*
+ * TODO: extend to a configurable database plugin mechanism where classes are
+ * instantiated by reflection and queried for their DbRefSource and version
+ * association.
*/
-public class SequenceFetcher extends ASequenceFetcher
+public class SequenceFetcher extends ASequenceFetcher implements ApplicationSingletonI
{
+ /*
+ * set a mock fetcher here for testing only - reset to null afterwards
+ */
+ private static SequenceFetcher mockFetcher;
+
+ /**
+ * Returns a new SequenceFetcher singleton, or a mock object if one has been
+ * set.
+ *
+ * @return
+ */
+ public static SequenceFetcher getInstance()
+ {
+ return mockFetcher != null ? mockFetcher
+ : (SequenceFetcher) ApplicationSingletonProvider
+ .getInstance(SequenceFetcher.class);
+ }
+
+ /**
+ * Set the instance object to use (intended for unit testing with mock
+ * objects).
+ *
+ * Be sure to reset to null in the tearDown method of any tests!
+ *
+ * @param sf
+ */
+ public static void setSequenceFetcher(SequenceFetcher sf)
+ {
+ mockFetcher = sf;
+ }
+
/**
- * Thread safe construction of database proxies TODO: extend to a configurable
- * database plugin mechanism where classes are instantiated by reflection and
- * queried for their DbRefSource and version association.
+ *
+ * This public constructor is only is for use by testng to anonymously
+ * subclass SequenceFetcher.
+ *
*
*/
public SequenceFetcher()
{
- addDBRefSourceImpl(EnsemblGene.class);
- // addDBRefSourceImpl(EnsemblGenomes.class);
- addDBRefSourceImpl(EmblSource.class);
- addDBRefSourceImpl(EmblCdsSource.class);
- addDBRefSourceImpl(Uniprot.class);
- addDBRefSourceImpl(Pdb.class);
- addDBRefSourceImpl(PfamFull.class);
- addDBRefSourceImpl(PfamSeed.class);
- addDBRefSourceImpl(RfamSeed.class);
+ addAllDatabases();
+ }
+
+ public void addAllDatabases()
+ {
+ addDBRefSourceImpl(EnsemblGene.class); // includes EnsemblGenomes.class
+ addDBRefSourceImpl(Uniprot.class); // includes UniprotName.class
+ // addDBRefSourceImpl(EmblSource.class);
+ // addDBRefSourceImpl(EmblCdsSource.class);
+ // addDBRefSourceImpl(Pdb.class);
+ // addDBRefSourceImpl(PfamFull.class);
+ // addDBRefSourceImpl(PfamSeed.class);
+ // addDBRefSourceImpl(RfamSeed.class);
+ addDBRefSourceImpl(DBRefSource.EMBL,
+ "jalview.ws.dbsources.EmblSource");
+ addDBRefSourceImpl(DBRefSource.EMBLCDS,
+ "jalview.ws.dbsources.EmblCdsSource");
+ addDBRefSourceImpl(DBRefSource.PDB, "jalview.ws.dbsources.Pdb");
+ addDBRefSourceImpl(DBRefSource.PFAM_FULL,
+ "jalview.ws.dbsources.PfamFull");
+ addDBRefSourceImpl(DBRefSource.PFAM_SEED,
+ "jalview.ws.dbsources.PfamSeed");
+ addDBRefSourceImpl(DBRefSource.RFAM_SEED,
+ "jalview.ws.dbsources.RfamSeed");
}
/**
- * return an ordered list of database sources excluding alignment only databases
+ * return an ordered list of database sources excluding alignment only
+ * databases
*/
public String[] getNonAlignmentSources()
{
String[] srcs = this.getSupportedDb();
List<String> src = new ArrayList<>();
-
- for (int i = 0; i < srcs.length; i++)
+ outer: for (int i = 0; i < srcs.length; i++)
{
- boolean accept = true;
for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
{
// Skip the alignment databases for the moment - they're not useful for
// verifying a single sequence against its reference source
if (dbs.isAlignmentSource())
{
- accept = false;
- break;
+ continue outer;
}
}
- if (accept)
- {
- src.add(srcs[i]);
- }
+ src.add(srcs[i]);
}
-
Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
return src.toArray(new String[src.size()]);
}
*/
package jalview.ws;
-import jalview.ws.seqfetcher.ASequenceFetcher;
-
public class SequenceFetcherFactory
{
-
- private static SequenceFetcher instance;
-
- /**
- * Returns a new SequenceFetcher object, or a mock object if one has been set
- *
- * @return
- */
- public static ASequenceFetcher getSequenceFetcher()
- {
- return instance == null ? new SequenceFetcher() : instance;
- }
-
- /**
- * Set the instance object to use (intended for unit testing with mock
- * objects).
- *
- * Be sure to reset to null in the tearDown method of any tests!
- *
- * @param sf
- */
- public static void setSequenceFetcher(SequenceFetcher sf)
- {
- instance = sf;
- }
+ // BH the two methods in this class merged into SequenceFetcher
}
*/
package jalview.ws.jws1;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.gui.JvOptionPane;
import jalview.util.MessageManager;
import ext.vamsas.ServiceHandle;
import ext.vamsas.ServiceHandles;
-public class Discoverer implements Runnable
+public class Discoverer implements Runnable, ApplicationSingletonI
{
- ext.vamsas.IRegistry registry; // the root registry service.
+
+ public static Discoverer getInstance()
+ {
+ return (Discoverer) ApplicationSingletonProvider.getInstance(Discoverer.class);
+ }
+
+ private Discoverer()
+ {
+ // use getInstance()
+ }
+
+ private java.net.URL RootServiceURL = null;
+
+ private Vector<URL> ServiceURLList = null;
+
+ private boolean reallyDiscoverServices = true;
+
+ private Hashtable<String, Vector<ServiceHandle>> services = null;
+
+ public Hashtable<String, Vector<ServiceHandle>> getServices()
+ {
+ return services;
+ }
+
+ private Vector<ServiceHandle> serviceList = null;
+
+ // private ext.vamsas.IRegistry registry; // the root registry service.
+
private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
this);
return server;
}
- static private java.net.URL RootServiceURL = null;
-
- static public Vector<URL> ServiceURLList = null;
-
- static private boolean reallyDiscoverServices = true;
-
- public static java.util.Hashtable<String, Vector<ServiceHandle>> services = null;
- // stored by
- // abstractServiceType
- // string
-
- public static java.util.Vector<ServiceHandle> serviceList = null;
-
static private Vector<URL> getDiscoveryURLS()
{
Vector<URL> urls = new Vector<>();
{
jalview.bin.Cache.log
.debug("(Re)-Initialising the discovery URL list.");
+ Discoverer d = getInstance();
try
{
- reallyDiscoverServices = jalview.bin.Cache
+ d.reallyDiscoverServices = jalview.bin.Cache
.getDefault("DISCOVERY_START", false);
- if (reallyDiscoverServices)
+ if (d.reallyDiscoverServices)
{
- ServiceURLList = getDiscoveryURLS();
+ d.ServiceURLList = getDiscoveryURLS();
}
else
{
jalview.bin.Cache.log.debug("Setting default services");
- services = new Hashtable<>();
+ d.services = new Hashtable<>();
// Muscle, Clustal and JPred.
- ServiceHandle[] defServices = { new ServiceHandle("MsaWS",
- "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment "
- + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
- "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
- MessageManager.getString(
- "label.muscle_multiple_protein_sequence_alignment")),
- new ServiceHandle("MsaWS",
- "Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) "
- + "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\""
- + " Nucleic Acids Research, 33 511-518",
- "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS",
- MessageManager.getString(
- "label.mafft_multiple_sequence_alignment")),
- new ServiceHandle("MsaWS",
- "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"
- + " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
- + " Nucleic Acids Research, 22 4673-4680",
- "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
- MessageManager.getString(
- "label.clustalw_multiple_sequence_alignment")),
- new ServiceHandle("SecStrPred",
- "Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)\nJPred4: a protein secondary structure prediction server"
- + "\nNucleic Acids Research, Web Server issue (first published 15th April 2015)"
- + "\ndoi://10.1093/nar/gkv332",
- "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred",
- "JPred Secondary Structure Prediction") };
- services = new Hashtable<>();
- serviceList = new Vector<>();
- buildServiceLists(defServices, serviceList, services);
+ ServiceHandle[] defServices = new ServiceHandle[0];
+ try
+ {
+ // BH 2020.03.18 issue with applet branch Module problem.
+ defServices = new ServiceHandle[] { new ServiceHandle("MsaWS",
+ "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment "
+ + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
+ MessageManager.getString(
+ "label.muscle_multiple_protein_sequence_alignment")),
+ new ServiceHandle("MsaWS",
+ "Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) "
+ + "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\""
+ + " Nucleic Acids Research, 33 511-518",
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS",
+ MessageManager.getString(
+ "label.mafft_multiple_sequence_alignment")),
+ new ServiceHandle("MsaWS",
+ "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"
+ + " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
+ + " Nucleic Acids Research, 22 4673-4680",
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
+ MessageManager.getString(
+ "label.clustalw_multiple_sequence_alignment")),
+ new ServiceHandle("SecStrPred",
+ "Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)\nJPred4: a protein secondary structure prediction server"
+ + "\nNucleic Acids Research, Web Server issue (first published 15th April 2015)"
+ + "\ndoi://10.1093/nar/gkv332",
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred",
+ "JPred Secondary Structure Prediction") };
+ } catch (Throwable e)
+ {
+
+ }
+ d.services = new Hashtable<>();
+ d.serviceList = new Vector<>();
+ buildServiceLists(defServices, d.serviceList, d.services);
}
} catch (Exception e)
{
System.err.println(
"jalview.rootRegistry is not a proper url!\nWas set to "
- + RootServiceURL + "\n" + e);
+ + d.RootServiceURL + "\n" + e);
}
}
// JBPNote - should do this a better way!
if (f.getFaultReason().indexOf("(407)") > -1)
{
- if (jalview.gui.Desktop.desktop != null)
+ if (jalview.gui.Desktop.getDesktopPane() != null)
{
- JvOptionPane.showMessageDialog(jalview.gui.Desktop.desktop,
+ JvOptionPane.showMessageDialog(jalview.gui.Desktop.getDesktopPane(),
MessageManager.getString("label.set_proxy_settings"),
MessageManager
.getString("label.proxy_authorization_failed"),
cat.add(sh[i]);
if (sh[i].getAbstractName().equals("Registry"))
{
- for (int s = 0, sUrls = ServiceURLList.size(); s < sUrls; s++)
+ Vector<URL> list = getInstance().ServiceURLList;
+ for (int s = 0, sUrls = list.size(); s < sUrls; s++)
{
java.net.URL disc_serv = null;
try
{
disc_serv = new java.net.URL(sh[i].getEndpointURL());
- if (!ServiceURLList.contains(disc_serv))
+ if (!list.contains(disc_serv))
{
jalview.bin.Cache.log.debug(
"Adding new discovery service at " + disc_serv);
- ServiceURLList.add(disc_serv);
+ list.add(disc_serv);
seenNewDiscovery = true;
}
} catch (Exception e)
} catch (Exception ex)
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.secondary_structure_prediction_service_couldnt_be_located",
new String[]
alignFrame = _alignFrame;
if (!sh.getAbstractName().equals("MsaWS"))
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.service_called_is_not_msa_service",
new String[]
if ((wsInfo = setWebService(sh)) == null)
{
- JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), MessageManager
.formatMessage("label.msa_service_is_unknown", new String[]
{ sh.getName() }),
MessageManager.getString("label.internal_jalview_error"),
// name to service client name
if (!sh.getAbstractName().equals(this.getServiceActionKey()))
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.service_called_is_not_seq_search_service",
new String[]
if ((wsInfo = setWebService(sh)) == null)
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.seq_search_service_is_unknown", new String[]
{ sh.getName() }),
{
// check service is actually in the list of currently avaialable
// services
- if (!Jws2Discoverer.getDiscoverer().getServices().contains(service))
+ if (!Jws2Discoverer.getInstance().getServices().contains(service))
{
// it isn't ..
service = null;
if (service == null)
{
// get the default service for AACon
- service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null,
+ service = Jws2Discoverer.getInstance().getPreferredServiceFor(null,
aaui.getServiceType());
}
if (service == null)
package jalview.ws.jws2;
import jalview.bin.Cache;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvSwingUtils;
* @author JimP
*
*/
-public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
+public class Jws2Discoverer
+ implements Runnable, WSMenuEntryProviderI, ApplicationSingletonI
{
+
+ /**
+ * Returns the singleton instance of this class.
+ *
+ * @return
+ */
+ public static Jws2Discoverer getInstance()
+ {
+ return (Jws2Discoverer) ApplicationSingletonProvider
+ .getInstance(Jws2Discoverer.class);
+ }
+
+ /**
+ * Private constructor enforces use of singleton via getDiscoverer()
+ */
+ private Jws2Discoverer()
+ {
+ // use getInstance();
+ }
+
public static final String COMPBIO_JABAWS = "http://www.compbio.dundee.ac.uk/jabaws";
/*
private final static String JWS2HOSTURLS = "JWS2HOSTURLS";
/*
- * Singleton instance
- */
- private static Jws2Discoverer discoverer;
-
- /*
* Override for testing only
*/
private static List<String> testUrls = null;
// preferred url has precedence over others
private String preferredUrl;
- private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+ protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
this);
private Vector<String> invalidServiceUrls = null;
protected Vector<Jws2Instance> services;
/**
- * Private constructor enforces use of singleton via getDiscoverer()
- */
- private Jws2Discoverer()
- {
- }
-
- /**
* change listeners are notified of "services" property changes
*
* @param listener
oldthread = Thread.currentThread();
try
{
- Class foo = getClass().getClassLoader()
+ getClass().getClassLoader()
.loadClass("compbio.ws.client.Jws2Client");
} catch (ClassNotFoundException e)
{
testUrls.add(url);
}
}
- Thread runner = getDiscoverer()
+ Thread runner = getInstance()
.startDiscoverer(new PropertyChangeListener()
{
@Override
public void propertyChange(PropertyChangeEvent evt)
{
- if (getDiscoverer().services != null)
+ if (getInstance().services != null)
{
System.out.println("Changesupport: There are now "
- + getDiscoverer().services.size() + " services");
+ + getInstance().services.size() + " services");
int i = 1;
- for (Jws2Instance instance : getDiscoverer().services)
+ for (Jws2Instance instance : getInstance().services)
{
System.out.println("Service " + i++ + " "
+ instance.getClass() + "@" + instance.getHost()
}
}
- /**
- * Returns the singleton instance of this class.
- *
- * @return
- */
- public static Jws2Discoverer getDiscoverer()
- {
- if (discoverer == null)
- {
- discoverer = new Jws2Discoverer();
- }
- return discoverer;
- }
-
public boolean hasServices()
{
return !running && services != null && services.size() > 0;
if (!(sh.service instanceof MsaWS))
{
// redundant at mo - but may change
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.service_called_is_not_msa_service",
new String[]
server = (MsaWS) sh.service;
if ((wsInfo = setWebService(sh, false)) == null)
{
- JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), MessageManager
.formatMessage("label.msa_service_is_unknown", new String[]
{ sh.serviceType }),
MessageManager.getString("label.internal_jalview_error"),
// dan changed! dan test. comment out if conditional
// if (alignFrame.getViewport().getAlignment().isNucleotide())
// {
- // JvOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
+ // JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), sh.serviceType
// + " can only be used\nfor amino acid alignments.",
// "Wrong type of sequences!", JvOptionPane.WARNING_MESSAGE);
// return;
@Override
public void actionPerformed(ActionEvent arg0)
{
- Desktop.instance.showUrl(service.docUrl);
+ Desktop.getInstance().showUrl(service.docUrl);
}
});
annotservice.setToolTipText(
try
{
paramStore = new JabaParamStore(this,
- (Desktop.instance != null ? Desktop.getUserParameterStore()
+ (Desktop.getInstance() != null ? Desktop.getUserParameterStore()
: null));
} catch (Exception ex)
{
else
{
// TODO: try to tell the user why the job couldn't be started.
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
(jobsthread.hasWarnings() ? jobsthread.getWarnings()
: MessageManager.getString(
"label.job_couldnt_be_started_check_input")),
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
import java.util.Stack;
import java.util.Vector;
/*
* set of databases we can retrieve entries from
*/
- protected Hashtable<String, Map<String, DbSourceProxy>> fetchableDbs;
+ protected Hashtable<String, Map<String, DbSourceProxyRoot>> fetchableDbs;
/*
* comparator to sort by tier (0/1/2) and name
*/
protected ASequenceFetcher()
{
- super();
-
/*
* comparator to sort proxies by tier and name
*/
public List<DbSourceProxy> getSourceProxy(String db)
{
db = DBRefUtils.getCanonicalName(db);
- Map<String, DbSourceProxy> dblist = fetchableDbs.get(db);
+ Map<String, DbSourceProxyRoot> dblist = fetchableDbs.get(db);
if (dblist == null)
{
return new ArrayList<>();
/*
* sort so that primary sources precede secondary
*/
- List<DbSourceProxy> dbs = new ArrayList<>(dblist.values());
+ List<DbSourceProxy> dbs = new ArrayList<>();
+ for (Entry<String, DbSourceProxyRoot> entry : dblist.entrySet())
+ {
+ DbSourceProxyRoot proxy = entry.getValue();
+ if (proxy instanceof DbRoot)
+ {
+ proxy = setProxy((DbRoot) proxy, dblist);
+ }
+ dbs.add((DbSourceProxy) proxy);
+ }
Collections.sort(dbs, proxyComparator);
return dbs;
}
+ class DbRoot implements DbSourceProxyRoot
+ {
+
+ private String sourceName;
+
+ private String className;
+
+ DbRoot(String sourceName, String className)
+ {
+ this.sourceName = sourceName;
+ this.className = className;
+ }
+
+ @Override
+ public String getDbSource()
+ {
+ return sourceName;
+ }
+
+ /**
+ * lazy class creation
+ *
+ * @return the actual proxy object
+ */
+ public DbSourceProxy getProxy()
+ {
+ try
+ {
+ return (DbSourceProxy) Class.forName(className).newInstance();
+ } catch (Exception e)
+ {
+ // Serious problems if this happens.
+ throw new Error(MessageManager.getString(
+ "error.dbrefsource_implementation_exception"), e);
+ }
+ }
+
+ }
+
/**
* constructs an instance of the proxy and registers it as a valid dbrefsource
*
- * @param dbSourceProxy
+ * @param dbSourceProxyClass
* reference for class implementing
* jalview.ws.seqfetcher.DbSourceProxy
*/
protected void addDBRefSourceImpl(
- Class<? extends DbSourceProxy> dbSourceProxy)
+ Class<? extends DbSourceProxy> dbSourceProxyClass)
throws IllegalArgumentException
{
DbSourceProxy proxy = null;
try
{
- DbSourceProxy proxyObj = dbSourceProxy.getConstructor().newInstance();
- proxy = proxyObj;
+ proxy = dbSourceProxyClass.getConstructor().newInstance();
} catch (IllegalArgumentException e)
{
throw e;
addDbRefSourceImpl(proxy);
}
+ public void addDBRefSourceImpl(String sourceName, String className)
+ {
+ addDbRefSourceImpl(new DbRoot(sourceName, className));
+ }
+
/**
* add the properly initialised DbSourceProxy object 'proxy' to the list of
* sequence fetchers
*
* @param proxy
*/
- protected void addDbRefSourceImpl(DbSourceProxy proxy)
+ void addDbRefSourceImpl(DbSourceProxyRoot proxy)
{
if (proxy != null)
{
{
fetchableDbs = new Hashtable<>();
}
- Map<String, DbSourceProxy> slist = fetchableDbs
- .get(proxy.getDbSource());
+ String key = proxy.getDbSource();
+ Map<String, DbSourceProxyRoot> slist = fetchableDbs.get(key);
if (slist == null)
{
- fetchableDbs.put(proxy.getDbSource(),
- slist = new Hashtable<>());
+ fetchableDbs.put(key, slist = new Hashtable<>());
+ }
+ if (proxy instanceof DbRoot)
+ {
+ slist.put("", proxy);
+ }
+ else
+ {
+ slist.put(((DbSourceProxy) proxy).getDbName(), proxy);
}
- slist.put(proxy.getDbName(), proxy);
}
}
/**
* select sources which are implemented by instances of the given class
*
- * @param class
+ * @param class1
* that implements DbSourceProxy
* @return null or vector of source names for fetchers
*/
- public String[] getDbInstances(Class class1)
+ public String[] getDbInstances(Class<?> class1)
{
if (!DbSourceProxy.class.isAssignableFrom(class1))
{
{
return null;
}
- String[] sources = null;
Vector<String> src = new Vector<>();
- Enumeration<String> dbs = fetchableDbs.keys();
- while (dbs.hasMoreElements())
+ for (String dbSource : fetchableDbs.keySet())
{
- String dbn = dbs.nextElement();
- for (DbSourceProxy dbp : fetchableDbs.get(dbn).values())
+ Map<String, DbSourceProxyRoot> dblist = fetchableDbs.get(dbSource);
+ for (Entry<String, DbSourceProxyRoot> entry : dblist.entrySet())
{
- if (class1.isAssignableFrom(dbp.getClass()))
+ DbSourceProxyRoot proxy = entry.getValue();
+ if (proxy instanceof DbRoot)
{
- src.addElement(dbn);
+ proxy = setProxy((DbRoot) proxy, dblist);
+ }
+ Class<?> c = proxy.getClass();
+ if (class1 == c || class1.isAssignableFrom(c))
+ {
+ src.addElement(dbSource);
}
}
}
+ String[] sources = null;
if (src.size() > 0)
{
src.copyInto(sources = new String[src.size()]);
return sources;
}
- public DbSourceProxy[] getDbSourceProxyInstances(Class class1)
+ private DbSourceProxyRoot setProxy(DbRoot root,
+ Map<String, DbSourceProxyRoot> dblist)
+ {
+ DbSourceProxy proxy = root.getProxy();
+ // Time to create the actual proxy
+ dblist.remove("");
+ dblist.put(proxy.getDbName(), proxy);
+ return proxy;
+ }
+
+ public DbSourceProxy[] getDbSourceProxyInstances(Class<?> class1)
{
+ if (fetchableDbs == null)
+ {
+ return null;
+ }
List<DbSourceProxy> prlist = new ArrayList<>();
- for (String fetchable : getSupportedDb())
+ for (String fetchable : fetchableDbs.keySet())
{
for (DbSourceProxy pr : getSourceProxy(fetchable))
{
--- /dev/null
+package jalview.ws.seqfetcher;
+
+public interface DbSourceProxyRoot
+{
+ /**
+ *
+ * @return source string constant used for this DB source
+ */
+ String getDbSource();
+
+}
public void setUp()
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.applicationProperties.setProperty("PAD_GAPS",
+ Cache.setPropertyNoSave("PAD_GAPS",
Boolean.FALSE.toString());
String seqData = "seq1seq1/8-18 ABCD--EF-GHIJI\n" + "seq2 A--BCDefHI\n"
public void setUp()
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Cache.setPropertyNoSave("STRUCT_FROM_PDB",
Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN",
+ Cache.setPropertyNoSave("ADD_TEMPFACT_ANN",
Boolean.FALSE.toString());
- Cache.applicationProperties.setProperty("ADD_SS_ANN",
+ Cache.setPropertyNoSave("ADD_SS_ANN",
Boolean.TRUE.toString());
StructureImportSettings.setDefaultStructureFileFormat("PDB");
StructureImportSettings
@AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
- jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+ jalview.gui.Desktop.getInstance().closeAll_actionPerformed(null);
}
@Test(groups = { "Functional" })
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.api;
+
+import jalview.datamodel.MappedFeatures;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSetI;
+
+import java.awt.Color;
+import java.awt.Graphics;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Abstract feature renderer interface
+ *
+ * @author JimP
+ *
+ */
+public interface FeatureRenderer
+{
+
+ /**
+ * Computes the feature colour for a given sequence and column position,
+ * taking into account sequence feature locations, feature colour schemes,
+ * render ordering, feature and feature group visibility, and transparency.
+ * <p>
+ * The graphics argument should be provided if transparency is applied
+ * (getTransparency() < 1). With feature transparency, visible features are
+ * written to the graphics context and the composite colour may be read off
+ * from it. In this case, the returned feature colour is not the composite
+ * colour but that of the last feature drawn.
+ * <p>
+ * If no transparency applies, then the graphics argument may be null, and the
+ * returned colour is the one that would be drawn for the feature.
+ * <p>
+ * Returns null if there is no visible feature at the position.
+ * <p>
+ * This is provided to support rendering of feature colours other than on the
+ * sequence alignment, including by structure viewers and the overview window.
+ * Note this method takes no account of whether the sequence or column is
+ * hidden.
+ *
+ * @param sequence
+ * @param column
+ * aligned column position (1..)
+ * @param g
+ * @return
+ */
+ Color findFeatureColour(SequenceI sequence, int column, Graphics g);
+
+ /**
+ * trigger the feature discovery process for a newly created feature renderer.
+ */
+ void featuresAdded();
+
+ /**
+ *
+ * @param ft
+ * @return display style for a feature
+ */
+ FeatureColourI getFeatureStyle(String ft);
+
+ /**
+ * update the feature style for a particular feature
+ *
+ * @param ft
+ * @param ggc
+ */
+ void setColour(String ft, FeatureColourI ggc);
+
+ AlignViewportI getViewport();
+
+ /**
+ *
+ * @return container managing list of feature types and their visibility
+ */
+ FeaturesDisplayedI getFeaturesDisplayed();
+
+ /**
+ * get display style for all features types - visible or invisible
+ *
+ * @return
+ */
+ Map<String, FeatureColourI> getFeatureColours();
+
+ /**
+ * query the alignment view to find all features
+ *
+ * @param newMadeVisible
+ * - when true, automatically make newly discovered types visible
+ */
+ void findAllFeatures(boolean newMadeVisible);
+
+ /**
+ * get display style for all features types currently visible
+ *
+ * @return
+ */
+ Map<String, FeatureColourI> getDisplayedFeatureCols();
+
+ /**
+ * get all registered groups
+ *
+ * @return
+ */
+ List<String> getFeatureGroups();
+
+ /**
+ * get groups that are visible/invisible
+ *
+ * @param visible
+ * @return
+ */
+ List<String> getGroups(boolean visible);
+
+ /**
+ * Set visibility for a list of groups
+ *
+ * @param toset
+ * @param visible
+ */
+ void setGroupVisibility(List<String> toset, boolean visible);
+
+ /**
+ * Set visibility of the given feature group
+ *
+ * @param group
+ * @param visible
+ */
+ void setGroupVisibility(String group, boolean visible);
+
+ /**
+ * Returns visible features at the specified aligned column on the given
+ * sequence. Non-positional features are not included. If the column has a gap,
+ * then enclosing features are included (but not contact features).
+ *
+ * @param sequence
+ * @param column
+ * aligned column position (1..)
+ * @return
+ */
+ List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column);
+
+ /**
+ * Returns features at the specified residue positions on the given sequence.
+ * Non-positional features are not included. Features are returned in render
+ * order of their feature type (last is on top). Within feature type, ordering
+ * is undefined.
+ *
+ * @param sequence
+ * @param fromResNo
+ * @param toResNo
+ * @return
+ */
+ List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence,
+ int fromResNo, int toResNo);
+
+ /**
+ * get current displayed types, in ordering of rendering (on top last)
+ *
+ * @return a (possibly empty) list of feature types
+ */
+
+ List<String> getDisplayedFeatureTypes();
+
+ /**
+ * Returns a (possibly empty) list of currently visible feature groups
+ *
+ * @return
+ */
+ List<String> getDisplayedFeatureGroups();
+
+ /**
+ * display all features of these types
+ *
+ * @param featureTypes
+ */
+ void setAllVisible(List<String> featureTypes);
+
+ /**
+ * display featureType
+ *
+ * @param featureType
+ */
+ void setVisible(String featureType);
+
+ /**
+ * Sets the transparency value, between 0 (full transparency) and 1 (no
+ * transparency)
+ *
+ * @param value
+ */
+ void setTransparency(float value);
+
+ /**
+ * Returns the transparency value, between 0 (full transparency) and 1 (no
+ * transparency)
+ *
+ * @return
+ */
+ float getTransparency();
+
+ /**
+ * Answers the filters applied to the given feature type, or null if none is
+ * set
+ *
+ * @param featureType
+ * @return
+ */
+ FeatureMatcherSetI getFeatureFilter(String featureType);
+
+ /**
+ * Answers the feature filters map
+ *
+ * @return
+ */
+ public Map<String, FeatureMatcherSetI> getFeatureFilters();
+
+ /**
+ * Sets the filters for the feature type, or removes them if a null or empty
+ * filter is passed
+ *
+ * @param featureType
+ * @param filter
+ */
+ void setFeatureFilter(String featureType, FeatureMatcherSetI filter);
+
+ /**
+ * Replaces all feature filters with the given map
+ *
+ * @param filters
+ */
+ void setFeatureFilters(Map<String, FeatureMatcherSetI> filters);
+
+ /**
+ * Returns the colour for a particular feature instance. This includes
+ * calculation of 'colour by label', or of a graduated score colour, if
+ * applicable.
+ * <p>
+ * Returns null if
+ * <ul>
+ * <li>feature group is not visible, or</li>
+ * <li>feature values lie outside any colour threshold, or</li>
+ * <li>feature is excluded by filter conditions</li>
+ * </ul>
+ * This method does not check feature type visibility.
+ *
+ * @param feature
+ * @return
+ */
+ Color getColour(SequenceFeature feature);
+
+ /**
+ * Answers true if feature would be shown, else false. A feature is shown if
+ * <ul>
+ * <li>its feature type is set to visible</li>
+ * <li>its feature group is either null, or set to visible</li>
+ * <li>it is not excluded by a colour threshold on score or other numeric
+ * attribute</li>
+ * <li>it is not excluded by a filter condition</li>
+ * </ul>
+ *
+ * @param feature
+ * @return
+ */
+ boolean isVisible(SequenceFeature feature);
+
+ /**
+ * Answers a bean containing a mapping, and a list of visible features in this
+ * alignment at a position (or range) which is mappable from the given sequence
+ * residue position in a mapped alignment. Features are returned in render order
+ * of feature type (on top last), with order within feature type undefined. If
+ * no features or mapping are found, answers null.
+ *
+ * @param sequence
+ * @param pos
+ * @return
+ */
+ MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence, int pos);
+}
@AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
}
@AfterMethod(alwaysRun = true)
@AfterMethod(alwaysRun = true)
public void tearDown()
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
}
/**
public void setUp()
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Cache.setPropertyNoSave("SHOW_IDENTITY",
Boolean.TRUE.toString());
af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
DataSourceType.FILE);
@Test(groups = { "Functional" }, timeOut=2000)
public void testUpdateConservation_qualityOnly()
{
- Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+ Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("SHOW_QUALITY",
+ Cache.setPropertyNoSave("SHOW_QUALITY",
Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Cache.setPropertyNoSave("SHOW_CONSERVATION",
Boolean.FALSE.toString());
- Cache.applicationProperties.setProperty("SHOW_OCCUPANCY",
+ Cache.setPropertyNoSave("SHOW_OCCUPANCY",
Boolean.FALSE.toString());
- Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Cache.setPropertyNoSave("SHOW_IDENTITY",
Boolean.FALSE.toString());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
/*
* test for JAL-2283: don't inadvertently turn on colour by conservation
*/
- Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "None");
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Cache.setPropertyNoSave("DEFAULT_COLOUR_PROT", "None");
+ Cache.setPropertyNoSave("SHOW_CONSERVATION",
Boolean.TRUE.toString());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
Jalview.main(new String[] { "-nonews", "-props",
"test/jalview/testProps.jvprops" });
- Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Cache.setPropertyNoSave("SHOW_IDENTITY",
Boolean.TRUE.toString());
af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
DataSourceType.FILE);
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
// pin down annotation sort order for test
- Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS,
+ Cache.setPropertyNoSave(Preferences.SORT_ANNOTATIONS,
SequenceAnnotationOrder.NONE.name());
final String TRUE = Boolean.TRUE.toString();
- Cache.applicationProperties.setProperty(
+ Cache.setPropertyNoSave(
Preferences.SHOW_AUTOCALC_ABOVE, TRUE);
- Cache.applicationProperties.setProperty("SHOW_QUALITY", TRUE);
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION", TRUE);
- Cache.applicationProperties.setProperty("SHOW_IDENTITY", TRUE);
+ Cache.setPropertyNoSave("SHOW_QUALITY", TRUE);
+ Cache.setPropertyNoSave("SHOW_CONSERVATION", TRUE);
+ Cache.setPropertyNoSave("SHOW_IDENTITY", TRUE);
AlignmentI al = new FormatAdapter().readFile(TEST_DATA,
DataSourceType.PASTE, FileFormat.Fasta);
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
// pin down annotation sort order for test
- Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS,
+ Cache.setPropertyNoSave(Preferences.SORT_ANNOTATIONS,
SequenceAnnotationOrder.NONE.name());
final String TRUE = Boolean.TRUE.toString();
- Cache.applicationProperties.setProperty(Preferences.SHOW_AUTOCALC_ABOVE,
+ Cache.setPropertyNoSave(Preferences.SHOW_AUTOCALC_ABOVE,
TRUE);
- Cache.applicationProperties.setProperty("SHOW_QUALITY", TRUE);
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION", TRUE);
- Cache.applicationProperties.setProperty("SHOW_IDENTITY", TRUE);
+ Cache.setPropertyNoSave("SHOW_QUALITY", TRUE);
+ Cache.setPropertyNoSave("SHOW_CONSERVATION", TRUE);
+ Cache.setPropertyNoSave("SHOW_IDENTITY", TRUE);
AlignmentI al = new FormatAdapter().readFile(TEST_DATA,
DataSourceType.PASTE, FileFormat.Fasta);
public void setUp()
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+ Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty(
+ Cache.setPropertyNoSave(
Preferences.SHOW_AUTOCALC_ABOVE, Boolean.TRUE.toString());
af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
DataSourceType.FILE);
{
// read-only Jalview properties
Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.applicationProperties.setProperty("BLOSUM62_PCA_FOR_NUCLEOTIDE",
+ Cache.setPropertyNoSave("BLOSUM62_PCA_FOR_NUCLEOTIDE",
Boolean.FALSE.toString());
}
/*
* enable inclusion of BLOSUM62 for nucleotide PCA (JAL-2962)
*/
- Cache.applicationProperties.setProperty("BLOSUM62_PCA_FOR_NUCLEOTIDE",
+ Cache.setPropertyNoSave("BLOSUM62_PCA_FOR_NUCLEOTIDE",
Boolean.TRUE.toString());
/*
Jalview.main(new String[] { "-nonews", "-props",
"test/jalview/testProps.jvprops" });
String True = Boolean.TRUE.toString();
- Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", True);
- Cache.applicationProperties.setProperty("SHOW_QUALITY", True);
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION", True);
- Cache.applicationProperties.setProperty("SHOW_OCCUPANCY", True);
- Cache.applicationProperties.setProperty("SHOW_IDENTITY", True);
+ Cache.setPropertyNoSave("SHOW_ANNOTATIONS", True);
+ Cache.setPropertyNoSave("SHOW_QUALITY", True);
+ Cache.setPropertyNoSave("SHOW_CONSERVATION", True);
+ Cache.setPropertyNoSave("SHOW_OCCUPANCY", True);
+ Cache.setPropertyNoSave("SHOW_IDENTITY", True);
}
/**
doStuffInJalview(f);
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
checkUsedMemory(35L);
}
* sanity check - fails if any frame was added after
* closeAll_actionPerformed
*/
- assertEquals(Desktop.instance.getAllFrames().length, 0);
+ assertEquals(Desktop.getInstance().getAllFrames().length, 0);
/*
* if this assertion fails
@AfterMethod(alwaysRun = true)
public void tearDown()
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
}
@Test(groups = "Functional")
public void testFindMousePosition_wrapped_annotations()
{
- Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "true");
- Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
+ Cache.setPropertyNoSave("SHOW_ANNOTATIONS", "true");
+ Cache.setPropertyNoSave("WRAP_ALIGNMENT", "true");
AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
AlignViewportI av = alignFrame.getViewport();
@Test(groups = "Functional")
public void testFindMousePosition_wrapped_scaleAbove()
{
- Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "true");
- Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
+ Cache.setPropertyNoSave("SHOW_ANNOTATIONS", "true");
+ Cache.setPropertyNoSave("WRAP_ALIGNMENT", "true");
AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
AlignViewportI av = alignFrame.getViewport();
@Test(groups = "Functional")
public void testFindMousePosition_wrapped_noAnnotations()
{
- Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "false");
- Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
+ Cache.setPropertyNoSave("SHOW_ANNOTATIONS", "false");
+ Cache.setPropertyNoSave("WRAP_ALIGNMENT", "true");
AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
AlignViewportI av = alignFrame.getViewport();
@Test(groups = "Functional")
public void testFindColumn_unwrapped()
{
- Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "false");
+ Cache.setPropertyNoSave("WRAP_ALIGNMENT", "false");
AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
@Test(groups = "Functional")
public void testFindColumn_wrapped()
{
- Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
+ Cache.setPropertyNoSave("WRAP_ALIGNMENT", "true");
AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
AlignViewport av = alignFrame.getViewport();
@BeforeMethod(alwaysRun = true)
public void setup() throws Exception
{
- Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Cache.setPropertyNoSave("STRUCT_FROM_PDB",
Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("ADD_SS_ANN",
+ Cache.setPropertyNoSave("ADD_SS_ANN",
Boolean.TRUE.toString());
FileLoader loader = new FileLoader(false);
AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
@AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
- jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+ jalview.gui.Desktop.getInstance().closeAll_actionPerformed(null);
}
}
else
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
// recover stored project
af = new FileLoader(false).LoadFileWaitTillLoaded(
savedProjects.get(first).toString(), DataSourceType.FILE);
}
else
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
pass3 = 0;
// recover stored project
File storedProject = savedProjects.get(nextxref);
}
else
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
// recover stored project
File storedProject = savedProjects.get(nextnextxref);
if (storedProject == null)
@AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
- jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+ jalview.gui.Desktop.getInstance().closeAll_actionPerformed(null);
}
@BeforeTest(alwaysRun = true)
if (Desktop.instance != null && Desktop.getFrames() != null
&& Desktop.getFrames().length > 0)
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
}
}
@AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
- jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+ jalview.gui.Desktop.getInstance().closeAll_actionPerformed(null);
}
@Test(groups = { "Functional" }, enabled = true)
public void testStoreAndRecoverExpandedviews() throws Exception
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
{
Assert.fail("Didn't save the expanded view state", e);
}
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
if (Desktop.getAlignFrames() != null)
{
Assert.assertEquals(Desktop.getAlignFrames().length, 0);
@Test(groups = { "Functional" })
public void testStoreAndRecoverReferenceSeqSettings() throws Exception
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
assertNotNull(af, "Didn't read in the example file correctly.");
{
Assert.fail("Didn't save the expanded view state", e);
}
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
if (Desktop.getAlignFrames() != null)
{
Assert.assertEquals(Desktop.getAlignFrames().length, 0);
@Test(groups = { "Functional" })
public void testStoreAndRecoverGroupRepSeqs() throws Exception
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
assertNotNull(af, "Didn't read in the example file correctly.");
{
Assert.fail("Didn't save the expanded view state", e);
}
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
if (Desktop.getAlignFrames() != null)
{
Assert.assertEquals(Desktop.getAlignFrames().length, 0);
@Test(groups = { "Functional" })
public void testStoreAndRecoverPDBEntry() throws Exception
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
String exampleFile = "examples/3W5V.pdb";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
DataSourceType.FILE);
{
Assert.fail("Didn't save the state", e);
}
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
if (Desktop.getAlignFrames() != null)
{
Assert.assertEquals(Desktop.getAlignFrames().length, 0);
@Test(groups = { "Functional" })
public void testStoreAndRecoverColourThresholds() throws IOException
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
".jvp");
tfile.deleteOnExit();
new Jalview2XML(false).saveState(tfile);
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
DataSourceType.FILE);
Assert.assertNotNull(af, "Failed to reload project");
@Test(groups = { "Functional" })
public void testMergeDatasetsforManyViews() throws IOException
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
// complex project - one dataset, several views on several alignments
AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
@Test(groups = "Functional")
public void testPcaViewAssociation() throws IOException
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
final String PCAVIEWNAME = "With PCA";
// create a new tempfile
File tempfile = File.createTempFile("jvPCAviewAssoc", "jvp");
}
// load again.
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
tempfile.getCanonicalPath(), DataSourceType.FILE);
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
+ JInternalFrame[] frames = Desktop.getInstance().getAllFrames();
// PCA and the tabbed alignment view should be the only two windows on the
// desktop
assertEquals(frames.length, 2,
@Test(groups = { "Functional" })
public void testStoreAndRecoverGeneLocus() throws Exception
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
String seqData = ">P30419\nACDE\n>X1235\nGCCTGTGACGAA";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
DataSourceType.PASTE);
{
Assert.fail("Didn't save the state", e);
}
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
DataSourceType.FILE);
@AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
}
@Test(groups = "Functional")
{
// for some reason 'BeforeMethod' (which should be inherited from
// Jalview2XmlBase isn't always called)...
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
try {
Thread.sleep(200);
} catch (Exception foo) {};
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
// ensure 'add annotation from structure' is selected
- Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Cache.setPropertyNoSave("STRUCT_FROM_PDB",
Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("ADD_SS_ANN",
+ Cache.setPropertyNoSave("ADD_SS_ANN",
Boolean.TRUE.toString());
sf = new SequenceFetcher();
@Test(groups = { "Network" }, enabled = true)
public void testRnaSeqRetrieve() throws Exception
{
- Cache.applicationProperties.setProperty("PDB_DOWNLOAD_FORMAT", "PDB");
+ Cache.setPropertyNoSave("PDB_DOWNLOAD_FORMAT", "PDB");
List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
assertTrue(response != null);
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
// ensure 'add annotation from structure' is selected
- Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Cache.setPropertyNoSave("STRUCT_FROM_PDB",
Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("ADD_SS_ANN",
+ Cache.setPropertyNoSave("ADD_SS_ANN",
Boolean.TRUE.toString());
sf = new SequenceFetcher();
public void setUp()
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Cache.setPropertyNoSave("STRUCT_FROM_PDB",
Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN",
+ Cache.setPropertyNoSave("ADD_TEMPFACT_ANN",
Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("ADD_SS_ANN",
+ Cache.setPropertyNoSave("ADD_SS_ANN",
Boolean.TRUE.toString());
StructureImportSettings.setDefaultStructureFileFormat("PDB");
}
git://source.jalview.org / jalview.git / commitdiff