*/
package jalview.bin;
+import jalview.api.AlignCalcWorkerI;
+import jalview.api.AlignViewportI;
+import jalview.api.JalviewApp;
+import jalview.api.StructureSelectionManagerProvider;
+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.AlignmentPanel;
+import jalview.gui.CalculationChooser;
import jalview.gui.Desktop;
import jalview.gui.PromptUserConfig;
+import jalview.gui.StructureViewer;
import jalview.io.AppletFormatAdapter;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
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 netscape.javascript.JSObject;
+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;
* @author $author$
* @version $Revision$
*/
-public class Jalview
+public class Jalview implements JalviewJSApi
{
static
{
public static AlignFrame currentAlignFrame;
+ public boolean isJavaAppletTag;
+
+ public String appletResourcePath;
+
+ JalviewAppLoader appLoader;
+
+ protected JSFunctionExec jsFunctionExec;
+
+ private boolean noCalculation, noMenuBar, noStatus;
+
+ private boolean noAnnotation;
+
+ public boolean getStartCalculations()
+ {
+ return !noCalculation;
+ }
+
+ public boolean getAllowMenuBar()
+ {
+ return !noMenuBar;
+ }
+
+ public boolean getShowStatus()
+ {
+ return !noStatus;
+ }
+
+ public boolean getShowAnnotation()
+ {
+ return !noAnnotation;
+ }
+
+
static
{
if (!Platform.isJS())
*/
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
- *
- */
+ if (false)
{
- System.out.println("not in js");
+ Platform.startJavaLogging();
}
- // 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");
- }
-
- }
-
-
-
+ instance = new Jalview();
+ instance.doMain(args);
+}
/**
* @param args
{
Jalview.currentAlignFrame = currentAlignFrame;
}
+
+ /**
+ * 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);
+ }
+
+ /**
+ * 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 getSelectedSequencesFrom(getCurrentAlignFrame());
+ }
+
+ /**
+ *
+ * @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(AlignFrame 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(AlignFrame 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(AlignFrame 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(AlignFrame alf, String sequenceIds, String columns)
+ {
+ selectIn(alf, sequenceIds, columns, null);
+ }
+
+ @Override
+ public void selectIn(AlignFrame 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(AlignFrame 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(AlignFrame alf)
+ {
+ return getAlignmentFrom(alf, null);
+ }
+
+ @Override
+ public String getAlignmentOrderFrom(AlignFrame 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(AlignFrame 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(AlignFrame 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(AlignFrame alf, String format,
+ String suffix)
+ {
+ return appLoader.getAlignmentFrom(alf, format, suffix);
+ }
+
+ @Override
+ public void loadAnnotation(String annotation)
+ {
+ loadAnnotationFrom(getCurrentAlignFrame(), annotation);
+ }
+
+ @Override
+ public void loadAnnotationFrom(AlignFrame 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(AlignFrame 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(AlignFrame alf, String format)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.getFeaturesFrom(alf, format);
+ }
+
+ @Override
+ public String getAnnotation()
+ {
+ return getAnnotationFrom(null);
+ }
+
+ @Override
+ public String getAnnotationFrom(AlignFrame alf)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.getAnnotationFrom(alf);
+ }
+
+// @Override
+// public AlignFrame newView()
+// {
+// return newViewFrom(null, null);
+// }
+//
+// @Override
+// public AlignFrame newView(String name)
+// {
+// return newViewFrom(null, name);
+// }
+//
+// @Override
+// public AlignFrame newViewFrom(AlignFrame alf)
+// {
+// return newViewFrom(alf, null);
+// }
+//
+// @Override
+// public AlignFrame newViewFrom(AlignFrame alf, String name)
+// {
+// if (alf == null)
+// {
+// alf = getCurrentAlignFrame();
+// }
+// return appLoader.newViewFrom(alf, name);
+// }
+
+ @Override
+ public AlignFrame loadAlignment(String text, String title)
+ {
+ return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT, title);
+ }
+
+ @Override
+ public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
+ String pdbEntryString, String pdbFile)
+ {
+ if (alFrame == null)
+ {
+ alFrame = getCurrentAlignFrame();
+ }
+ return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString,
+ pdbFile);
+ }
+
+ @Override
+ public void scrollViewToIn(AlignFrame alf, String topRow,
+ String leftHandColumn)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ appLoader.scrollViewToIn(alf, topRow, leftHandColumn);
+ }
+
+ @Override
+ public void scrollViewToRowIn(AlignFrame alf, String topRow)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ appLoader.scrollViewToRowIn(alf, topRow);
+ }
+
+ @Override
+ public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ appLoader.scrollViewToColumnIn(alf, leftHandColumn);
+ }
+
+ @Override
+ public String getFeatureGroups()
+ {
+ return getFeatureGroupsOn(null);
+ }
+
+ @Override
+ public String getFeatureGroupsOn(AlignFrame alf)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.getFeatureGroupsOn(alf);
+ }
+
+ @Override
+ public String getFeatureGroupsOfState(boolean visible)
+ {
+ return getFeatureGroupsOfStateOn(null, visible);
+ }
+
+ @Override
+ public String getFeatureGroupsOfStateOn(AlignFrame 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(AlignFrame alf, String groups,
+ boolean state)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ appLoader.setFeatureGroupStateOn(alf, groups, state);
+ }
+
+ @Override
+ public String getSeparator()
+ {
+ 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(AlignFrame 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(AlignFrame af, String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setSelectionListener(String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setSelectionListener(AlignFrame 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(AlignFrame 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);
+ }
+
+ @Override
+ public Object parseArguments(String[] args)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+
+
+
}
--- /dev/null
+package jalview.bin;
+
+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.awt.EventQueue;
+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(AlignFrame alf, String sep)
+ {
+ StringBuffer result = new StringBuffer("");
+ if (sep == null || sep.length() == 0)
+ {
+ sep = separator; // "+0x00AC;
+ }
+ AlignViewport v = 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 AlignFrame alf,
+ final String groups, boolean state)
+ {
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ alf.setFeatureGroupState(
+ separatorListToArray(groups, separator), state);
+ }
+ });
+ }
+
+ public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
+ {
+ return arrayToSeparatorList(
+ alf.getFeatureGroupsOfState(visible));
+ }
+
+ public void scrollViewToIn(final AlignFrame alf, final String topRow,
+ final String leftHandColumn)
+ {
+ // TODO test
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ alf.scrollTo(Integer.valueOf(topRow).intValue(),
+ Integer.valueOf(leftHandColumn).intValue());
+
+ } catch (Exception ex)
+ {
+ System.err.println("Couldn't parse integer arguments (topRow='"
+ + topRow + "' and leftHandColumn='" + leftHandColumn
+ + "')");
+ ex.printStackTrace();
+ }
+ }
+ });
+ }
+
+ public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
+ {
+ // TODO test
+
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ alf.scrollToRow(Integer.valueOf(topRow).intValue());
+
+ } catch (Exception ex)
+ {
+ System.err.println("Couldn't parse integer arguments (topRow='"
+ + topRow + "')");
+ ex.printStackTrace();
+ }
+
+ }
+ });
+ }
+
+ public void scrollViewToColumnIn(final AlignFrame alf,
+ final String leftHandColumn)
+ {
+ // TODO test
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ alf
+ .scrollToColumn(Integer.valueOf(leftHandColumn).intValue());
+
+ } catch (Exception ex)
+ {
+ System.err.println(
+ "Couldn't parse integer arguments (leftHandColumn='"
+ + leftHandColumn + "')");
+ ex.printStackTrace();
+ }
+ }
+ });
+
+ }
+
+ public boolean addPdbFile(AlignFrame alf, String sequenceId,
+ String pdbEntryString, String pdbFile)
+ {
+ AlignFrame alFrame = 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 AlignFrame 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(AlignFrame alf)
+ {
+ return arrayToSeparatorList(
+ alf.getFeatureGroups());
+ }
+
+ public void highlightIn(final AlignFrame 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.getViewport().getAlignment()
+ .getSequencesArray());
+ final SequenceI sq = matcher.findIdMatch(sequenceId);
+ if (sq != null)
+ {
+ int apos = -1;
+ try
+ {
+ apos = Integer.valueOf(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))
+ {
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ StructureSelectionManager
+ .getStructureSelectionManager(Desktop.getInstance())
+ .mouseOverVamsasSequence(sq, sq.findIndex(pos), null);
+ }
+ });
+ }
+ else
+ {
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ StructureSelectionManager
+ .getStructureSelectionManager(Desktop.getInstance())
+ .mouseOverVamsasSequence(sq, pos, null);
+ }
+ });
+ }
+ }
+ }
+
+ public void selectIn(final AlignFrame 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 = alf.getViewport().getAlignment();
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ 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 = Integer.valueOf(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 = Integer.valueOf(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 = Integer.valueOf(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);
+ EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ alf.select(sel, csel, alf
+ .getCurrentView().getAlignment().getHiddenColumns());
+ }
+ });
+ }
+ }
+
+ public String getAlignmentOrderFrom(AlignFrame alf, String sep)
+ {
+ AlignmentI alorder = 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(AlignFrame alf,
+ String format, String suffix)
+ {
+ try
+ {
+ AlignViewport vp = 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(AlignFrame 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(
+ 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 alf.sortBy(aorder, _undoName) ? "true" : "";
+ }
+
+ public String getAlignmentFrom(AlignFrame 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,
+ alf.getViewport().getAlignment(), seqlimits);
+ return reply;
+ } catch (IllegalArgumentException ex)
+ {
+ ex.printStackTrace();
+ return "Error retrieving alignment, possibly invalid format specifier: "
+ + format;
+ }
+ }
+
+ public void loadAnnotationFrom(AlignFrame alf, String annotation)
+ {
+ if (new AnnotationFile().annotateAlignmentView(
+ alf.getViewport(), annotation,
+ DataSourceType.PASTE))
+ {
+ alf.alignPanel.fontChanged();
+ alf.alignPanel.setScrollValues(0, 0);
+ }
+ else
+ {
+ alf.parseFeaturesFile(annotation,
+ DataSourceType.PASTE);
+ }
+ }
+
+ public boolean loadFeaturesFrom(AlignFrame alf, String features,
+ boolean autoenabledisplay)
+ {
+ boolean ret = alf.parseFeaturesFile(features,
+ DataSourceType.PASTE);
+ if (!ret)
+ {
+ return false;
+ }
+ if (autoenabledisplay)
+ {
+ alf.getViewport().setShowSequenceFeatures(true);
+ // this next was for a checkbox in JalviewLite
+ // ((AlignFrame) alf).getViewport().sequenceFeatures.setState(true);
+ }
+ return true;
+ }
+
+ /**
+ * JavaScript interface to print the alignment frame
+ *
+ * @param alf
+ * @param format
+ * "jalview" or "gff" with or without ";includeComplement" or
+ * ";includeNonpositional"; default with no ";" is
+ * ";includeNonpositional"
+ * @return
+ */
+ public String getFeaturesFrom(AlignFrame alf, String format)
+ {
+ AlignFrame f = (alf);
+
+ String features;
+ FeaturesFile formatter = new FeaturesFile();
+ format = format.toLowerCase();
+ if (format.indexOf(";") < 0)
+ format += ";includenonpositional";
+ boolean nonpos = format.indexOf(";includenonpositional") > 0;
+ boolean compl = format.indexOf(";includecomplement") >= 0;
+ if (format.startsWith("jalview"))
+ {
+ features = formatter.printJalviewFormat(
+ f.getViewport().getAlignment().getSequencesArray(),
+ f.alignPanel.getFeatureRenderer(), nonpos, compl);
+ }
+ else
+ {
+ features = formatter.printGffFormat(
+ f.getViewport().getAlignment().getSequencesArray(),
+ f.alignPanel.getFeatureRenderer(), nonpos, compl);
+ }
+
+ if (features == null)
+ {
+ features = "";
+ }
+ return features;
+
+ }
+
+ public String getAnnotationFrom(AlignFrame alf)
+ {
+ AlignFrame f = alf;
+ String annotation = new AnnotationFile()
+ .printAnnotationsForView(f.getViewport());
+ return annotation;
+ }
+
+ // public AlignFrame newViewFrom(AlignFrame alf, String name)
+ // {
+ // return (AlignFrame) alf.newView(name, true);
+ // }
+ //
+ public String[] separatorListToArray(String list)
+ {
+ return separatorListToArray(list, separator);
+ }
+
+ public Object[] getSelectionForListener(AlignFrame 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
+ && currentFrame.getViewport() == source)
+ {
+ // should be valid if it just generated an event!
+ src = 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
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;
}
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(
frameTitle += this.title;
- Desktop.addInternalFrame(tp, frameTitle, 600, 500);
+ Dimension dim = Platform.getDimIfEmbedded(tp, 600, 500);
+ Desktop.addInternalFrame(tp, frameTitle, dim.width, dim.height);
}
/**
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)
{
*
* @return
*/
- public static Object getInstance()
+ public static Desktop getInstance()
{
return instance;
}
frame.setMaximizable(resizable);
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);
protected boolean draggingBox = false;
+ private Dimension dim;
+
+ private boolean showProgress = !Platform.isJS();
+
protected ProgressPanel progressPanel;
+
/**
- * Creates a new OverviewPanel object.
- *
- * @param alPanel
- * The alignment panel which is shown in the overview panel
+ * Creates the appropriate type of OverviewDimensions, with the desired size
*/
- public OverviewPanel(AlignmentPanel alPanel)
+ private void createOverviewDimensions()
{
- this.av = alPanel.av;
- this.ap = alPanel;
-
- showHidden = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
- false);
+ boolean showAnnotation = (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null);
if (showHidden)
{
- od = new OverviewDimensionsShowHidden(av.getRanges(),
- (av.isShowAnnotation()
- && av.getAlignmentConservationAnnotation() != null));
+ od = new OverviewDimensionsShowHidden(av.getRanges(), showAnnotation,
+ dim);
}
else
{
- od = new OverviewDimensionsHideHidden(av.getRanges(),
- (av.isShowAnnotation()
- && av.getAlignmentConservationAnnotation() != null));
+ od = new OverviewDimensionsHideHidden(av.getRanges(), showAnnotation,
+ dim);
}
+ }
+ public OverviewPanel(AlignmentPanel alPanel, Dimension dim)
+ {
+ this.av = alPanel.av;
+ this.ap = alPanel;
+ this.dim = dim;
+
+ showHidden = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
+ false);
+ createOverviewDimensions();
setLayout(new BorderLayout());
progressPanel = new ProgressPanel(OverviewRenderer.UPDATE,
MessageManager.getString("label.oview_calc"), getWidth());
*/
protected void toggleHiddenColumns()
{
- if (showHidden)
- {
- showHidden = false;
- od = new OverviewDimensionsHideHidden(av.getRanges(),
- (av.isShowAnnotation()
- && av.getAlignmentConservationAnnotation() != null));
- }
- else
- {
- showHidden = true;
- od = new OverviewDimensionsShowHidden(av.getRanges(),
- (av.isShowAnnotation()
- && av.getAlignmentConservationAnnotation() != null));
- }
+ showHidden = !showHidden;
+ createOverviewDimensions();
oviewCanvas.resetOviewDims(od);
updateOverviewImage();
setBoxPosition();
import jalview.math.RotatableMatrix.Axis;
import jalview.util.ImageMaker;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.PCAModel;
repaint();
if (getParent() == null)
{
- Desktop.addInternalFrame(this,
- MessageManager.formatMessage("label.calc_title", "PCA",
- getPcaModel().getScoreModelName()),
- 475, 450);
+ addToDesktop(this, getPcaModel().getScoreModelName());
this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
}
working = false;
getRotatableCanvas().ap = panel;
PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId());
}
+
+ public static void addToDesktop(PCAPanel panel, String modelName)
+ {
+ Dimension dim = Platform.getDimIfEmbedded(panel, 475, 450);
+ Desktop.addInternalFrame(panel, MessageManager.formatMessage(
+ "label.calc_title", "PCA", modelName), dim.width,
+ dim.height);
+ }
}
*/
package jalview.io;
+import java.awt.Dimension;
import java.io.File;
import java.io.IOException;
import java.util.StringTokenizer;
import jalview.schemes.ColourSchemeI;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.ws.utils.UrlDownloadClient;
public class FileLoader implements Runnable
// 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
import jalview.analysis.GeneticCodes;
import jalview.api.SplitContainerI;
import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
import jalview.io.FileFormats;
{
// for Web-page embedding using id=align-frame-div
- setName("jalview-alignment");
+ setName(Jalview.getAppID("alignment"));
+
jbInit();
setJMenuBar(alignFrameMenuBar);
package jalview.jbgui;
import jalview.api.AlignmentViewPanel;
+import jalview.bin.Jalview;
import jalview.io.FileFormatException;
import jalview.util.MessageManager;
import jalview.util.Platform;
*/
private void jbInit() throws Exception
{
- setName("jalview-desktop");
+
+ setName(Jalview.getAppID("desktop"));
FileMenu.setText(MessageManager.getString("action.file"));
HelpMenu.setText(MessageManager.getString("action.help"));
inputLocalFileMenuItem
*/
package jalview.jbgui;
+import jalview.bin.Jalview;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
private void jbInit() throws Exception
{
- setName("jalview-pca");
+ setName(Jalview.getAppID("pca"));
this.getContentPane().setLayout(new BorderLayout());
JPanel jPanel2 = new JPanel();
jPanel2.setLayout(new FlowLayout());
package jalview.jbgui;
import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Jalview;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
private void jbInit() throws Exception
{
- setName("jalview-structureviewer");
+ setName(Jalview.getAppID("structureviewer"));
JMenuBar menuBar = new JMenuBar();
this.setJMenuBar(menuBar);
*/
package jalview.jbgui;
+import jalview.bin.Jalview;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
private void jbInit() throws Exception
{
- setName("jalview-tree");
+ setName(Jalview.getAppID("tree"));
this.getContentPane().setLayout(borderLayout1);
this.setBackground(Color.white);
this.setFont(new java.awt.Font("Verdana", 0, 12));
import jalview.xml.binding.jalview.VAMSAS;
import java.awt.Color;
+import java.awt.Dimension;
import java.awt.Font;
import java.awt.Rectangle;
import java.io.BufferedReader;
String complementaryViewId = view.getComplementId();
if (complementaryViewId == null)
{
- Desktop.addInternalFrame(af, view.getTitle(),
+ Dimension dim = Platform.getDimIfEmbedded(af,
safeInt(view.getWidth()), safeInt(view.getHeight()));
+ Desktop.addInternalFrame(af, view.getTitle(), dim.width, dim.height);
// recompute any autoannotation
af.alignPanel.updateAnnotation(false, true);
reorderAutoannotation(af, al, autoAlan);
panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
axis.getXPos(), axis.getYPos(), axis.getZPos());
}
-
- Desktop.addInternalFrame(panel, MessageManager.formatMessage(
- "label.calc_title", "PCA", modelName), 475, 450);
+ PCAPanel.addToDesktop(panel, modelName);
}
} catch (Exception ex)
{
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
+import java.awt.Dimension;
import java.awt.Graphics;
public abstract class OverviewDimensions
* true if the annotation panel is to be shown, false otherwise
*/
public OverviewDimensions(ViewportRanges ranges,
- boolean showAnnotationPanel)
+ boolean showAnnotationPanel, Dimension dim)
{
+ if (!showAnnotationPanel)
+ {
+ graphHeight = 0;
+ }
+
// scale the initial size of overviewpanel to shape of alignment
float initialScale = (float) ranges.getAbsoluteAlignmentWidth()
/ (float) ranges.getAbsoluteAlignmentHeight();
- if (!showAnnotationPanel)
+ if (dim != null)
{
- graphHeight = 0;
+ width = dim.width;
+ sequencesHeight = dim.height;
+ return;
}
if (ranges.getAbsoluteAlignmentWidth() > ranges
*/
package jalview.viewmodel;
+import java.awt.Dimension;
+
import jalview.api.AlignmentColsCollectionI;
import jalview.api.AlignmentRowsCollectionI;
import jalview.datamodel.AlignmentI;
private int ydiff; // when dragging, difference in alignment units between
// start sequence and original mouse click position
+ /**
+ * for testng only
+ *
+ * @param vpranges
+ * @param showAnnotationPanel
+ */
+ @Deprecated
+ public OverviewDimensionsHideHidden(ViewportRanges vpranges, boolean showAnnotationPanel) {
+ this(vpranges, showAnnotationPanel, null);
+ }
+
public OverviewDimensionsHideHidden(ViewportRanges vpranges,
- boolean showAnnotationPanel)
+ boolean showAnnotationPanel, Dimension dim)
{
- super(vpranges, showAnnotationPanel);
+ super(vpranges, showAnnotationPanel, dim);
ranges = vpranges;
resetAlignmentDims();
}
*/
package jalview.viewmodel;
+import java.awt.Dimension;
+
import jalview.api.AlignmentColsCollectionI;
import jalview.api.AlignmentRowsCollectionI;
import jalview.datamodel.AlignmentI;
private int ydiff; // when dragging, difference in alignment units between
// start sequence and original mouse click position
+
+ /**
+ * for testng only
+ *
+ * @param vpranges
+ * @param showAnnotationPanel
+ */
+ @Deprecated
+ public OverviewDimensionsShowHidden(ViewportRanges vpranges, boolean showAnnotationPanel) {
+ this(vpranges, showAnnotationPanel, null);
+ }
+
/**
* Create an OverviewDimensions object
*
* true if the annotation panel is to be shown, false otherwise
*/
public OverviewDimensionsShowHidden(ViewportRanges vpranges,
- boolean showAnnotationPanel)
+ boolean showAnnotationPanel, Dimension dim)
{
- super(vpranges, showAnnotationPanel);
+ super(vpranges, showAnnotationPanel, dim);
ranges = vpranges;
resetAlignmentDims();
}
git://source.jalview.org / jalview.git / commitdiff