X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarna.java;h=3a647169a8eb2ead5c32b31e7536cee61c0703d2;hb=4d959452a9c486b6d94291d8e819036ec19b09ef;hp=beb4980cd87f4a582e910410056e8f7007b9658f;hpb=21fccb30635d61dbf7ad0f266a88f07fb87358f7;p=jalview.git diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java index beb4980..3a64716 100644 --- a/src/jalview/gui/AppVarna.java +++ b/src/jalview/gui/AppVarna.java @@ -20,16 +20,30 @@ */ package jalview.gui; +import jalview.analysis.AlignSeq; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.RnaViewerModel; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.ext.varna.RnaModel; +import jalview.structure.SecondaryStructureListener; +import jalview.structure.SelectionListener; +import jalview.structure.SelectionSource; +import jalview.structure.StructureSelectionManager; +import jalview.structure.VamsasSource; +import jalview.util.Comparison; +import jalview.util.MessageManager; +import jalview.util.ShiftList; + import java.awt.BorderLayout; import java.awt.Color; -import java.lang.reflect.InvocationTargetException; import java.util.Collection; import java.util.Hashtable; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; -import java.util.regex.Matcher; -import java.util.regex.Pattern; import javax.swing.JInternalFrame; import javax.swing.JSplitPane; @@ -47,28 +61,12 @@ import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation; import fr.orsay.lri.varna.models.rna.ModeleBase; import fr.orsay.lri.varna.models.rna.RNA; -import jalview.analysis.AlignSeq; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.ColumnSelection; -import jalview.datamodel.RnaViewerModel; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.ext.varna.RnaModel; -import jalview.structure.SecondaryStructureListener; -import jalview.structure.SelectionListener; -import jalview.structure.SelectionSource; -import jalview.structure.StructureSelectionManager; -import jalview.structure.VamsasSource; -import jalview.util.Comparison; -import jalview.util.MessageManager; -import jalview.util.ShiftList; - -public class AppVarna extends JInternalFrame implements SelectionListener, - SecondaryStructureListener, InterfaceVARNASelectionListener, - VamsasSource +public class AppVarna extends JInternalFrame + implements SelectionListener, SecondaryStructureListener, + InterfaceVARNASelectionListener, VamsasSource { - private static final Pattern PAIRS_PATTERN = Pattern - .compile("[^([{<>}])]"); + private static final byte[] PAIRS = new byte[] { '(', ')', '[', ']', '{', + '}', '<', '>' }; private AppVarnaBinding vab; @@ -122,6 +120,15 @@ public class AppVarna extends JInternalFrame implements SelectionListener, } } + /** + * highlight a region from start to end (inclusive) on rna + * + * @param rna + * @param start + * - first base pair index (from 0) + * @param end + * - last base pair index (from 0) + */ public void highlightRegion(RNA rna, int start, int end) { clearLastSelection(); @@ -179,23 +186,24 @@ public class AppVarna extends JInternalFrame implements SelectionListener, { this(ap); - String sname = aa.sequenceRef == null ? "secondary structure (alignment)" + String sname = aa.sequenceRef == null + ? "secondary structure (alignment)" : seq.getName() + " structure"; String theTitle = sname - + (aa.sequenceRef == null ? " trimmed to " + seq.getName() : ""); + + (aa.sequenceRef == null ? " trimmed to " + seq.getName() + : ""); theTitle = MessageManager.formatMessage("label.varna_params", new String[] { theTitle }); setTitle(theTitle); String gappedTitle = sname + " (with gaps)"; - RnaModel gappedModel = new RnaModel(gappedTitle, aa, seq, null, true, - null); + RnaModel gappedModel = new RnaModel(gappedTitle, aa, seq, null, true); addModel(gappedModel, gappedTitle); String trimmedTitle = "trimmed " + sname; RnaModel trimmedModel = new RnaModel(trimmedTitle, aa, seq, null, - false, null); + false); addModel(trimmedModel, trimmedTitle); vab.setSelectedIndex(0); } @@ -262,13 +270,6 @@ public class AppVarna extends JInternalFrame implements SelectionListener, showPanel(true); } - public String replaceOddGaps(String oldStr) - { - Matcher matcher = PAIRS_PATTERN.matcher(oldStr); - String newStr = matcher.replaceAll("."); - return newStr; - } - /** * Constructs a new RNA model from the given one, without gaps. Also * calculates and saves a 'shift list' @@ -284,7 +285,8 @@ public class AppVarna extends JInternalFrame implements SelectionListener, RNA rnaTrim = new RNA(name); try { - rnaTrim.setRNA(rna.getSeq(), replaceOddGaps(rna.getStructDBN())); + String structDBN = rna.getStructDBN(true); + rnaTrim.setRNA(rna.getSeq(), replaceOddGaps(structDBN)); } catch (ExceptionUnmatchedClosingParentheses e2) { e2.printStackTrace(); @@ -295,7 +297,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener, String seq = rnaTrim.getSeq(); StringBuilder struc = new StringBuilder(256); - struc.append(rnaTrim.getStructDBN()); + struc.append(rnaTrim.getStructDBN(true)); int ofstart = -1; int sleng = seq.length(); @@ -308,7 +310,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener, ofstart = i; } /* - * mark base or base pair in the structure with * + * mark base or base & pair in the structure with * */ if (!rnaTrim.findPair(i).isEmpty()) { @@ -404,15 +406,8 @@ public class AppVarna extends JInternalFrame implements SelectionListener, RnaModel rnaModel = models.get(rna); if (rnaModel.seq == sequence) { - int highlightPos = rnaModel.gapped ? index : position - 1; - // int highlightPos = index; - // ShiftList shift = offsets.get(rna); - // if (shift != null) - // { - // System.err.print("Orig pos:" + index); - // highlightPos = shift.shift(index); - // System.err.println("\nFinal pos:" + index); - // } + int highlightPos = rnaModel.gapped ? index + : position - sequence.getStart(); mouseOverHighlighter.highlightRegion(rna, highlightPos, highlightPos); vab.updateSelectedRNA(rna); } @@ -420,7 +415,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener, @Override public void selection(SequenceGroup seqsel, ColumnSelection colsel, - SelectionSource source) + HiddenColumns hidden, SelectionSource source) { if (source != ap.av) { @@ -433,18 +428,31 @@ public class AppVarna extends JInternalFrame implements SelectionListener, { return; } - if (seqsel != null && seqsel.getSize() > 0) + + RnaModel rnaModel = models.get(rna); + + if (seqsel != null && seqsel.getSize() > 0 + && seqsel.contains(rnaModel.seq)) { int start = seqsel.getStartRes(), end = seqsel.getEndRes(); - ShiftList shift = offsets.get(rna); - if (shift != null) + if (rnaModel.gapped) { - start = shift.shift(start); - end = shift.shift(end); + ShiftList shift = offsets.get(rna); + if (shift != null) + { + start = shift.shift(start); + end = shift.shift(end); + } } + else + { + start = rnaModel.seq.findPosition(start) - rnaModel.seq.getStart(); + end = rnaModel.seq.findPosition(end) - rnaModel.seq.getStart(); + } + selectionHighlighter.highlightRegion(rna, start, end); - selectionHighlighter.getLastHighlight().setOutlineColor( - seqsel.getOutlineColour()); + selectionHighlighter.getLastHighlight() + .setOutlineColor(seqsel.getOutlineColour()); // TODO - translate column markings to positions on structure if present. vab.updateSelectedRNA(rna); } @@ -479,7 +487,8 @@ public class AppVarna extends JInternalFrame implements SelectionListener, } @Override - public void onSelectionChanged(BaseList arg0, BaseList arg1, BaseList arg2) + public void onSelectionChanged(BaseList arg0, BaseList arg1, + BaseList arg2) { // TODO translate selected regions in VARNA to a selection on the // alignpanel. @@ -596,35 +605,8 @@ public class AppVarna extends JInternalFrame implements SelectionListener, { if (!model.ann.isValidStruc()) { - throw new IllegalArgumentException("Invalid RNA structure annotation"); - } - - /* - * loaded from project file with Varna session data - */ - if (model.varnaSession != null) - { - try - { - FullBackup fromSession = vab.vp.loadSession(model.varnaSession); - vab.addStructure(fromSession.rna, fromSession.config); - RNA rna = fromSession.rna; - // copy the model, but now including the RNA object - RnaModel newModel = new RnaModel(model.title, model.ann, model.seq, - rna, model.gapped, model.varnaSession); - if (!model.gapped) - { - registerOffset(rna, buildOffset(model.seq)); - } - models.put(rna, newModel); - // capture rna selection state when saved - selectionHighlighter = new VarnaHighlighter(rna); - return fromSession.rna; - } catch (ExceptionLoadingFailed e) - { - e.printStackTrace(); - return null; - } + throw new IllegalArgumentException( + "Invalid RNA structure annotation"); } /* @@ -651,7 +633,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener, rna = trimRNA(rna, modelName); } models.put(rna, new RnaModel(modelName, model.ann, model.seq, rna, - model.gapped, null)); + model.gapped)); vab.addStructure(rna); return rna; } @@ -669,11 +651,10 @@ public class AppVarna extends JInternalFrame implements SelectionListener, ShiftList offset = new ShiftList(); int ofstart = -1; int sleng = seq.getLength(); - char[] seqChars = seq.getSequence(); for (int i = 0; i < sleng; i++) { - if (Comparison.isGap(seqChars[i])) + if (Comparison.isGap(seq.getCharAt(i))) { if (ofstart == -1) { @@ -701,10 +682,101 @@ public class AppVarna extends JInternalFrame implements SelectionListener, /** * Set the selected index in the model selection list * - * @param selectedR + * @param selectedIndex */ public void setInitialSelection(final int selectedIndex) { + /* + * empirically it needs a second for Varna/AWT to finish loading/drawing + * models for this to work; SwingUtilities.invokeLater _not_ a solution; + * explanation and/or better solution welcome! + */ + synchronized (this) + { + try + { + wait(1000); + } catch (InterruptedException e) + { + // meh + } + } vab.setSelectedIndex(selectedIndex); } + + /** + * Add a model with associated Varna session file + * + * @param rna + * @param modelName + */ + public RNA addModelSession(RnaModel model, String modelName, + String sessionFile) + { + if (!model.ann.isValidStruc()) + { + throw new IllegalArgumentException( + "Invalid RNA structure annotation"); + } + + try + { + FullBackup fromSession = vab.vp.loadSession(sessionFile); + vab.addStructure(fromSession.rna, fromSession.config); + RNA rna = fromSession.rna; + // copy the model, but now including the RNA object + RnaModel newModel = new RnaModel(model.title, model.ann, model.seq, + rna, model.gapped); + if (!model.gapped) + { + registerOffset(rna, buildOffset(model.seq)); + } + models.put(rna, newModel); + // capture rna selection state when saved + selectionHighlighter = new VarnaHighlighter(rna); + return fromSession.rna; + } catch (ExceptionLoadingFailed e) + { + System.err + .println("Error restoring Varna session: " + e.getMessage()); + return null; + } + } + + /** + * Replace everything except RNA secondary structure characters with a period + * + * @param s + * @return + */ + public static String replaceOddGaps(String s) + { + if (s == null) + { + return null; + } + + // this is measured to be 10 times faster than a regex replace + boolean changed = false; + byte[] bytes = s.getBytes(); + for (int i = 0; i < bytes.length; i++) + { + boolean ok = false; + // todo check for ((b >= 'a' && b <= 'z') || (b >= 'A' && b <= 'Z')) if + // wanted also + for (int j = 0; !ok && (j < PAIRS.length); j++) + { + if (bytes[i] == PAIRS[j]) + { + ok = true; + } + } + if (!ok) + { + bytes[i] = '.'; + changed = true; + } + } + return changed ? new String(bytes) : s; + } }