package jalview.gui;
import jalview.analysis.AlignmentSorter;
-import jalview.analysis.NJTree;
-import jalview.analysis.scoremodels.ScoreModels;
-import jalview.analysis.scoremodels.SimilarityParams;
-import jalview.api.analysis.ScoreModelI;
-import jalview.api.analysis.ViewBasedAnalysisI;
+import jalview.analysis.TreeModel;
import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.OrderCommand;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
-import jalview.datamodel.ColumnSelection;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.NodeTransformI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
*/
public class TreePanel extends GTreePanel
{
- String type;
+ String substitutionMatrix;
- String pwtype;
+ String treeType;
+
+ String treeTitle; // if tree loaded
TreeCanvas treeCanvas;
- NJTree tree;
+ TreeModel tree;
AlignViewport av;
/**
* Creates a new TreePanel object.
*
- * @param av
- * DOCUMENT ME!
- * @param seqVector
- * DOCUMENT ME!
- * @param type
- * DOCUMENT ME!
- * @param pwtype
- * DOCUMENT ME!
- * @param s
- * DOCUMENT ME!
- * @param e
- * DOCUMENT ME!
+ * @param ap
+ * @param tree
+ * @param treeType
+ * @param substitutionMatrix
*/
- public TreePanel(AlignmentPanel ap, String type, String pwtype)
+ public TreePanel(AlignmentPanel ap, TreeModel tree, String treeType,
+ String substitutionMatrix)
{
super();
- initTreePanel(ap, type, pwtype, null, null);
+ this.treeType = treeType;
+ this.substitutionMatrix = substitutionMatrix;
+ this.tree = tree;
+ initTreePanel(ap, tree);
// We know this tree has distances. JBPNote TODO: prolly should add this as
// a userdefined default
// showDistances(true);
}
- public TreePanel(AlignmentPanel av, String type, String pwtype,
- NewickFile newtree, AlignmentView inputData)
+ /**
+ * Creates a new TreePanel object.
+ *
+ * @param alignPanel
+ * @param newtree
+ * @param theTitle
+ * @param inputData
+ */
+ public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
+ String theTitle, AlignmentView inputData)
{
super();
- initTreePanel(av, type, pwtype, newtree, inputData);
+ this.treeTitle = theTitle;
+ initTreePanel(alignPanel, newtree, inputData);
}
public AlignmentI getAlignment()
return treeCanvas.av;
}
- void initTreePanel(AlignmentPanel ap, String type, String pwtype,
- NewickFile newTree, AlignmentView inputData)
+ /**
+ * Initialize a tree panel based on a calculated tree
+ *
+ * @param ap
+ * @param tree
+ */
+ void initTreePanel(AlignmentPanel ap, TreeModel tree)
+ {
+ buildTreeCanvas(ap);
+
+ TreeLoader tl = new TreeLoader(null, null);
+ tl.start();
+
+ }
+
+ /**
+ * Initialize a tree panel based on a loaded in tree file.
+ *
+ * @param ap
+ * @param loadedTree
+ * @param inputData
+ */
+ void initTreePanel(AlignmentPanel ap,
+ NewickFile loadedTree, AlignmentView inputData)
{
+ buildTreeCanvas(ap);
- av = ap.av;
- this.type = type;
- this.pwtype = pwtype;
+ TreeLoader tl = new TreeLoader(loadedTree, inputData);
+ tl.start();
+ }
+
+public void buildTreeCanvas(AlignmentPanel ap) {
+ av = ap.av;
treeCanvas = new TreeCanvas(this, ap, scrollPane);
scrollPane.setViewportView(treeCanvas);
+
PaintRefresher.Register(this, ap.av.getSequenceSetId());
buildAssociatedViewMenu();
}
if (evt.getNewValue() == null)
{
- System.out
- .println("new alignment sequences vector value is null");
+ System.out.println(
+ "new alignment sequences vector value is null");
}
tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
}
});
- TreeLoader tl = new TreeLoader(newTree);
- if (inputData != null)
- {
- tl.odata = inputData;
- }
- tl.start();
+
+
}
void buildAssociatedViewMenu()
{
- AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
- .getSequenceSetId());
+ AlignmentPanel[] aps = PaintRefresher
+ .getAssociatedPanels(av.getSequenceSetId());
if (aps.length == 1 && treeCanvas.ap == aps[0])
{
associateLeavesMenu.setVisible(false);
associateLeavesMenu.setVisible(true);
- if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+ if ((viewMenu
+ .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
{
viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
}
class TreeLoader extends Thread
{
- NewickFile newtree;
+ private NewickFile newTree;
- jalview.datamodel.AlignmentView odata = null;
+ private AlignmentView odata = null;
- public TreeLoader(NewickFile newtree)
+ public TreeLoader(NewickFile newickFile, AlignmentView inputData)
{
- this.newtree = newtree;
- if (newtree != null)
+ this.newTree = newickFile;
+ this.odata = inputData;
+
+ if (newTree != null)
{
// Must be outside run(), as Jalview2XML tries to
// update distance/bootstrap visibility at the same time
- showBootstrap(newtree.HasBootstrap());
- showDistances(newtree.HasDistances());
+ showBootstrap(newTree.hasBootstrap());
+ showDistances(newTree.hasDistances());
+
}
+
}
@Override
public void run()
{
- if (newtree != null)
- {
- if (odata == null)
- {
- tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
- }
- else
- {
- tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
- newtree);
- }
- if (!tree.hasOriginalSequenceData())
- {
- allowOriginalSeqData(false);
- }
- }
- else
+ if (newTree != null)
{
- int start, end;
- SequenceI[] seqs;
- boolean selview = av.getSelectionGroup() != null
- && av.getSelectionGroup().getSize() > 1;
- AlignmentView seqStrings = av.getAlignmentView(selview);
- if (!selview)
- {
- start = 0;
- end = av.getAlignment().getWidth();
- seqs = av.getAlignment().getSequencesArray();
- }
- else
+ tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
+ newTree);
+ if (tree.getOriginalData() == null)
{
- start = av.getSelectionGroup().getStartRes();
- end = av.getSelectionGroup().getEndRes() + 1;
- seqs = av.getSelectionGroup().getSequencesInOrder(
- av.getAlignment());
+ originalSeqData.setVisible(false);
}
- ScoreModelI sm = configureScoreModel(pwtype);
- tree = new NJTree(av, type, sm, SimilarityParams.Jalview);
- showDistances(true);
+
+
+
}
+ showTree(tree);
+ }
+
+ public void showTree(TreeModel tree)
+ {
tree.reCount(tree.getTopNode());
tree.findHeight(tree.getTopNode());
treeCanvas.setTree(tree);
treeCanvas.repaint();
+
av.setCurrentTree(tree);
if (av.getSortByTree())
{
sortByTree_actionPerformed();
}
+
}
}
treeCanvas.setMarkPlaceholders(b);
}
- private void allowOriginalSeqData(boolean b)
- {
- originalSeqData.setVisible(b);
- }
-
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public NJTree getTree()
+ public TreeModel getTree()
{
return tree;
}
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
- String newTitle = getPanelTitle(type, pwtype);
+ String newTitle = getPanelTitle();
NewickFile fout = new NewickFile(tree.getTopNode());
try
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.save_tree_as_newick"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.save_tree_as_newick"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(null);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
try
{
jalview.io.NewickFile fout = new jalview.io.NewickFile(
tree.getTopNode());
- String output = fout.print(tree.hasBootstrap(),
- tree.hasDistances(), tree.hasRootDistance());
+ String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
+ tree.hasRootDistance());
java.io.PrintWriter out = new java.io.PrintWriter(
new java.io.FileWriter(choice));
out.println(output);
@Override
public void originalSeqData_actionPerformed(ActionEvent e)
{
- if (!tree.hasOriginalSequenceData())
+ AlignmentView originalData = tree.getOriginalData();
+ if (originalData == null)
{
- jalview.bin.Cache.log
- .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+ jalview.bin.Cache.log.info(
+ "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
// decide if av alignment is sufficiently different to original data to
} catch (Exception ex)
{
}
- ;
- Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
+
+ Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
if (alAndColsel != null && alAndColsel[0] != null)
{
// AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
- AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
- .getAlignment().getDataset() : null;
+ AlignmentI dataset = (av != null && av.getAlignment() != null)
+ ? av.getAlignment().getDataset()
+ : null;
if (dataset != null)
{
al.setDataset(dataset);
if (true)
{
// make a new frame!
- AlignFrame af = new AlignFrame(al,
- (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
// >>>This is a fix for the moment, until a better solution is
// found!!<<<
// msaorder);
Desktop.addInternalFrame(af, MessageManager.formatMessage(
- "label.original_data_for_params",
- new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH,
+ "label.original_data_for_params", new Object[]
+ { this.title }), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
}
* @param e
*/
@Override
- public void sortByTree_actionPerformed()
+ public void sortByTree_actionPerformed()// modify for Aptx
{
if (treeCanvas.applyToAllViews)
{
- final ArrayList<CommandI> commands = new ArrayList<CommandI>();
- for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
- .getSequenceSetId()))
+ final ArrayList<CommandI> commands = new ArrayList<>();
+ for (AlignmentPanel ap : PaintRefresher
+ .getAssociatedPanels(av.getSequenceSetId()))
{
commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
}
}
}
});
- for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
- .getSequenceSetId()))
+ for (AlignmentPanel ap : PaintRefresher
+ .getAssociatedPanels(av.getSequenceSetId()))
{
// ensure all the alignFrames refresh their GI after adding an undo item
ap.alignFrame.updateEditMenuBar();
public CommandI sortAlignmentIn(AlignmentPanel ap)
{
- AlignmentViewport av = ap.av;
- SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
- AlignmentSorter.sortByTree(av.getAlignment(), tree);
+ // TODO: move to alignment view controller
+ AlignmentViewport viewport = ap.av;
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
CommandI undo;
- undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
+ undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
- ap.paintAlignment(true);
+ ap.paintAlignment(true, false);
return undo;
}
return treeCanvas.font;
}
- public void setTreeFont(Font font)
+ public void setTreeFont(Font f)
{
if (treeCanvas != null)
{
- treeCanvas.setFont(font);
+ treeCanvas.setFont(f);
}
}
JalviewFileChooser chooser = new JalviewFileChooser(
ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.create_eps_from_tree"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.create_eps_from_tree"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
return;
}
- Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile()
- .getParent());
+ Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
- EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
+ FileOutputStream out = new FileOutputStream(
+ chooser.getSelectedFile());
+ EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
+ height);
pg.setAccurateTextMode(accurateText);
ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.create_png_from_tree"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.create_png_from_tree"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
return;
}
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+ FileOutputStream out = new FileOutputStream(
+ chooser.getSelectedFile());
BufferedImage bi = new BufferedImage(width, height,
BufferedImage.TYPE_INT_RGB);
if (sq != null)
{
// search dbrefs, features and annotation
- DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
- sq.getDBRefs(),
- new String[] { labelClass.toUpperCase() });
+ DBRefEntry[] refs = jalview.util.DBRefUtils
+ .selectRefs(sq.getDBRefs(), new String[]
+ { labelClass.toUpperCase() });
if (refs != null)
{
for (int i = 0; i < refs.length; i++)
}
if (newname == null)
{
- SequenceFeature sf[] = sq.getSequenceFeatures();
- for (int i = 0; sf != null && i < sf.length; i++)
+ List<SequenceFeature> features = sq.getFeatures()
+ .getPositionalFeatures(labelClass);
+ for (SequenceFeature feature : features)
{
- if (sf[i].getType().equals(labelClass))
+ if (newname == null)
+ {
+ newname = feature.getDescription();
+ }
+ else
{
- if (newname == null)
- {
- newname = new String(sf[i].getDescription());
- }
- else
- {
- newname = newname + "; " + sf[i].getDescription();
- }
+ newname = newname + "; " + feature.getDescription();
}
}
}
}
if (newname != null)
{
- String oldname = ((SequenceNode) node).getName();
- // TODO : save in the undo object for this modification.
+ // String oldname = ((SequenceNode) node).getName();
+ // TODO : save oldname in the undo object for this modification.
((SequenceNode) node).setName(newname);
}
}
* <p>
* For a tree loaded from file, just uses the file name
*
- * @param treeType
- * NJ or AV or FromFile
- * @param modelOrFileName
* @return
*/
- public static String getPanelTitle(String treeType, String modelOrFileName)
+ public String getPanelTitle() // to be moved/fixed
{
- if (NJTree.FROM_FILE.equals(treeType))
+ if (treeTitle != null)
{
- return modelOrFileName;
+ return treeTitle;
}
-
- /*
- * i18n description of Neighbour Joining or Average Distance method
- */
- String treecalcnm = MessageManager.getString("label.tree_calc_"
- + treeType.toLowerCase());
-
- /*
- * i18n description (if any) of score model used
- */
- String smn = MessageManager.getStringOrReturn("label.score_model_",
- modelOrFileName);
-
- /*
- * put them together as <method> Using <model>
- */
- final String ttl = MessageManager.formatMessage("label.treecalc_title",
- treecalcnm, smn);
- return ttl;
- }
-
- /**
- * Gets the score model for the given name. If the score model is one that
- * requires to get state data from the current view, allow it to do so
- *
- * @param sm
- * @return
- */
- protected ScoreModelI configureScoreModel(String modelName)
- {
- ScoreModelI sm = ScoreModels.getInstance().forName(modelName);
- if (sm instanceof ViewBasedAnalysisI)
+ else
{
- try
- {
- sm = sm.getClass().newInstance();
- ((ViewBasedAnalysisI) sm).configureFromAlignmentView(treeCanvas.ap);
- } catch (Exception q)
- {
- Cache.log.error("Couldn't create a scoremodel instance for "
- + sm.getName());
- }
+ /*
+ * i18n description of Neighbour Joining or Average Distance method
+ */
+ String treecalcnm = MessageManager
+ .getString("label.tree_calc_" + treeType.toLowerCase());
+
+ /*
+ * short score model name (long description can be too long)
+ */
+ String smn = substitutionMatrix;
+
+ /*
+ * put them together as <method> Using <model>
+ */
+ final String ttl = MessageManager
+ .formatMessage("label.treecalc_title", treecalcnm, smn);
+ return ttl;
}
- return sm;
}
}
git://source.jalview.org / jalview.git / blobdiff