X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=6a8db59b513e17c947747f71d294eaa6e0950c61;hb=af83e7d123133d2bb44b0bcafe538e300304a1b1;hp=dbc707d387ca807e2fc9dc9397694767d0d96feb;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index dbc707d..6a8db59 100644 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -31,7 +31,6 @@ 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; @@ -46,10 +45,12 @@ import jalview.io.IdentifyFile; import jalview.io.JPredFile; import jalview.io.JnetAnnotationMaker; import jalview.io.NewickFile; -import jalview.javascript.JSFunctionExec; -import jalview.javascript.JalviewLiteJsApi; -import jalview.javascript.JsCallBack; -import jalview.javascript.MouseOverStructureListener; +import jalview.appletgui.js.JSFunctionExec; +import jalview.appletgui.js.JalviewLiteJsApi; +import jalview.appletgui.js.JsCallBack; +import jalview.appletgui.js.JsSelectionSender; +import jalview.appletgui.js.MouseOverListener; +import jalview.appletgui.js.MouseOverStructureListener; import jalview.structure.SelectionListener; import jalview.structure.StructureSelectionManager; import jalview.util.ColorUtils; @@ -85,8 +86,8 @@ import netscape.javascript.JSObject; * @author $author$ * @version $Revision: 1.92 $ */ -public class JalviewLite extends Applet implements - StructureSelectionManagerProvider, JalviewLiteJsApi +public class JalviewLite extends Applet + implements StructureSelectionManagerProvider, JalviewLiteJsApi { private static final String TRUE = "true"; @@ -199,7 +200,7 @@ public class JalviewLite extends Applet implements int apos = -1; try { - apos = new Integer(position).intValue(); + apos = Integer.valueOf(position).intValue(); apos--; } catch (NumberFormatException ex) { @@ -208,9 +209,8 @@ public class JalviewLite extends Applet implements final StructureSelectionManagerProvider me = this; 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)) + if (alignedPosition != null && (alignedPosition.trim().length() == 0 + || alignedPosition.toLowerCase().indexOf("false") > -1)) { java.awt.EventQueue.invokeLater(new Runnable() { @@ -339,23 +339,23 @@ public class JalviewLite extends Applet implements int from = -1, to = -1; try { - from = new Integer(cl.substring(0, p)).intValue(); + 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 '" + System.err.println( + "ERROR: Couldn't parse first integer in range element column selection string '" + cl + "' - format is 'from-to'"); return; } try { - to = new Integer(cl.substring(p + 1)).intValue(); + to = 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 '" + System.err.println( + "ERROR: Couldn't parse second integer in range element column selection string '" + cl + "' - format is 'from-to'"); return; } @@ -410,7 +410,7 @@ public class JalviewLite extends Applet implements int r = -1; try { - r = new Integer(cl).intValue(); + r = Integer.valueOf(cl).intValue(); r--; } catch (NumberFormatException ex) { @@ -421,8 +421,8 @@ public class JalviewLite extends Applet implements } else { - System.err - .println("ERROR: Couldn't parse integer from point selection element of column selection string '" + System.err.println( + "ERROR: Couldn't parse integer from point selection element of column selection string '" + cl + "'"); return; } @@ -472,7 +472,7 @@ public class JalviewLite extends Applet implements SequenceI rs = sel.getSequenceAt(0); start = rs.findIndex(start); end = rs.findIndex(end); - List cs = new ArrayList(csel.getSelected()); + List cs = new ArrayList<>(csel.getSelected()); csel.clear(); for (Integer selectedCol : cs) { @@ -486,8 +486,8 @@ public class JalviewLite extends Applet implements @Override public void run() { - alf.select(sel, csel, alf.getAlignViewport().getAlignment() - .getHiddenColumns()); + alf.select(sel, csel, + alf.getAlignViewport().getAlignment().getHiddenColumns()); } }); } @@ -501,7 +501,8 @@ public class JalviewLite extends Applet implements * String, java.lang.String) */ @Override - public String getSelectedSequencesAsAlignment(String format, String suffix) + public String getSelectedSequencesAsAlignment(String format, + String suffix) { return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(), format, suffix); @@ -921,7 +922,7 @@ public class JalviewLite extends Applet implements setMouseoverListener(currentAlignFrame, listener); } - private Vector javascriptListeners = new Vector(); + private Vector javascriptListeners = new Vector<>(); /* * (non-Javadoc) @@ -938,12 +939,12 @@ public class JalviewLite extends Applet implements listener = listener.trim(); if (listener.length() == 0) { - System.err - .println("jalview Javascript error: Ignoring empty function for mouseover listener."); + System.err.println( + "jalview Javascript error: Ignoring empty function for mouseover listener."); return; } } - jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener( + MouseOverListener mol = new MouseOverListener( this, af, listener); javascriptListeners.addElement(mol); StructureSelectionManager.getStructureSelectionManager(this) @@ -951,8 +952,9 @@ public class JalviewLite extends Applet implements if (debug) { System.err.println("Added a mouseover listener for " - + ((af == null) ? "All frames" : "Just views for " - + af.getAlignViewport().getSequenceSetId())); + + ((af == null) ? "All frames" + : "Just views for " + + af.getAlignViewport().getSequenceSetId())); System.err.println("There are now " + javascriptListeners.size() + " listeners in total."); } @@ -984,12 +986,12 @@ public class JalviewLite extends Applet implements listener = listener.trim(); if (listener.length() == 0) { - System.err - .println("jalview Javascript error: Ignoring empty function for selection listener."); + System.err.println( + "jalview Javascript error: Ignoring empty function for selection listener."); return; } } - jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender( + JsSelectionSender mol = new JsSelectionSender( this, af, listener); javascriptListeners.addElement(mol); StructureSelectionManager.getStructureSelectionManager(this) @@ -997,8 +999,9 @@ public class JalviewLite extends Applet implements if (debug) { System.err.println("Added a selection listener for " - + ((af == null) ? "All frames" : "Just views for " - + af.getAlignViewport().getSequenceSetId())); + + ((af == null) ? "All frames" + : "Just views for " + + af.getAlignViewport().getSequenceSetId())); System.err.println("There are now " + javascriptListeners.size() + " listeners in total."); } @@ -1023,8 +1026,8 @@ public class JalviewLite extends Applet implements listener = listener.trim(); if (listener.length() == 0) { - System.err - .println("jalview Javascript error: Ignoring empty function for selection listener."); + System.err.println( + "jalview Javascript error: Ignoring empty function for selection listener."); return; } } @@ -1065,9 +1068,8 @@ public class JalviewLite extends Applet implements { Object lstn = javascriptListeners.elementAt(ms); JsCallBack lstner = (JsCallBack) lstn; - if ((af == null || lstner.getAlignFrame() == af) - && (listener == null || lstner.getListenerFunction().equals( - listener))) + if ((af == null || lstner.getAlignFrame() == af) && (listener == null + || lstner.getListenerFunction().equals(listener))) { javascriptListeners.removeElement(lstner); msSize--; @@ -1128,7 +1130,7 @@ public class JalviewLite extends Applet implements { while (javascriptListeners.size() > 0) { - jalview.javascript.JSFunctionExec mol = javascriptListeners + JSFunctionExec mol = javascriptListeners .elementAt(0); javascriptListeners.removeElement(mol); if (mol instanceof SelectionListener) @@ -1155,7 +1157,7 @@ public class JalviewLite extends Applet implements StructureSelectionManager.release(this); } - private jalview.javascript.JSFunctionExec jsFunctionExec; + private JSFunctionExec jsFunctionExec; /* * (non-Javadoc) @@ -1164,8 +1166,8 @@ public class JalviewLite extends Applet implements * java.lang.String, java.lang.String) */ @Override - public void mouseOverStructure(final String pdbResNum, - final String chain, final String pdbfile) + public void mouseOverStructure(final String pdbResNum, final String chain, + final String pdbfile) { final StructureSelectionManagerProvider me = this; java.awt.EventQueue.invokeLater(new Runnable() @@ -1176,13 +1178,13 @@ public class JalviewLite extends Applet implements try { StructureSelectionManager.getStructureSelectionManager(me) - .mouseOverStructure(new Integer(pdbResNum).intValue(), + .mouseOverStructure(Integer.valueOf(pdbResNum).intValue(), chain, pdbfile); if (debug) { - System.err.println("mouseOver for '" + pdbResNum - + "' in chain '" + chain + "' in structure '" + pdbfile - + "'"); + System.err + .println("mouseOver for '" + pdbResNum + "' in chain '" + + chain + "' in structure '" + pdbfile + "'"); } } catch (NumberFormatException e) { @@ -1212,8 +1214,8 @@ public class JalviewLite extends Applet implements { try { - alf.scrollTo(new Integer(topRow).intValue(), new Integer( - leftHandColumn).intValue()); + alf.scrollTo(Integer.valueOf(topRow).intValue(), + Integer.valueOf(leftHandColumn).intValue()); } catch (Exception ex) { @@ -1230,7 +1232,7 @@ public class JalviewLite extends Applet implements * (non-Javadoc) * * @see - * jalview.javascript.JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui + * JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui * .AlignFrame, java.lang.String) */ @Override @@ -1244,7 +1246,7 @@ public class JalviewLite extends Applet implements { try { - alf.scrollToRow(new Integer(topRow).intValue()); + alf.scrollToRow(Integer.valueOf(topRow).intValue()); } catch (Exception ex) { @@ -1261,7 +1263,7 @@ public class JalviewLite extends Applet implements * (non-Javadoc) * * @see - * jalview.javascript.JalviewLiteJsApi#scrollViewToColumnIn(jalview.appletgui + * JalviewLiteJsApi#scrollViewToColumnIn(jalview.appletgui * .AlignFrame, java.lang.String) */ @Override @@ -1276,12 +1278,12 @@ public class JalviewLite extends Applet implements { try { - alf.scrollToColumn(new Integer(leftHandColumn).intValue()); + alf.scrollToColumn(Integer.valueOf(leftHandColumn).intValue()); } catch (Exception ex) { - System.err - .println("Couldn't parse integer arguments (leftHandColumn='" + System.err.println( + "Couldn't parse integer arguments (leftHandColumn='" + leftHandColumn + "')"); ex.printStackTrace(); } @@ -1333,7 +1335,7 @@ public class JalviewLite extends Applet implements private boolean alignPdbStructures = false; /** - * use an external structure viewer exclusively (no jmols or MCViews will be + * use an external structure viewer exclusively (no jmols or mc_views will be * opened by JalviewLite itself) */ public boolean useXtrnalSviewer = false; @@ -1355,8 +1357,8 @@ public class JalviewLite extends Applet implements { try { - BufferedReader reader = new BufferedReader(new InputStreamReader( - url.openStream())); + BufferedReader reader = new BufferedReader( + new InputStreamReader(url.openStream())); String line; while ((line = reader.readLine()) != null) { @@ -1423,8 +1425,8 @@ public class JalviewLite extends Applet implements } catch (Exception ex) { - System.err - .println("Warning: No JalviewLite javascript callbacks available."); + System.err.println( + "Warning: No JalviewLite javascript callbacks available."); if (debug) { ex.printStackTrace(); @@ -1466,9 +1468,8 @@ public class JalviewLite extends Applet implements } else { - throw new Error( - MessageManager - .getString("error.invalid_separator_parameter")); + throw new Error(MessageManager + .getString("error.invalid_separator_parameter")); } } int r = 255; @@ -1625,8 +1626,8 @@ public class JalviewLite extends Applet implements { // do onInit with the JS executor thread new JSFunctionExec(this).executeJavascriptFunction(true, - initjscallback, null, "Calling oninit callback '" - + initjscallback + "'."); + initjscallback, null, + "Calling oninit callback '" + initjscallback + "'."); } catch (Exception e) { System.err.println("Exception when executing _oninit callback '" @@ -1737,8 +1738,8 @@ public class JalviewLite extends Applet implements g.fillRect(0, 0, getSize().width, getSize().height); g.setColor(Color.red); g.drawString( - MessageManager.getString("label.jalview_cannot_open_file"), - 5, 15); + MessageManager.getString("label.jalview_cannot_open_file"), 5, + 15); g.drawString("\"" + file + "\"", 5, 30); } else if (embedded) @@ -1798,8 +1799,8 @@ public class JalviewLite extends Applet implements } if (!jmolAvailable) { - System.out - .println("Jmol not available - Using MCview for structures"); + System.out.println( + "Jmol not available - Using mc_view for structures"); } } catch (java.lang.ClassNotFoundException ex) { @@ -1810,8 +1811,8 @@ public class JalviewLite extends Applet implements jmolAvailable = false; if (debug) { - System.err - .println("Skipping Jmol check. Will use MCView (probably)"); + System.err.println( + "Skipping Jmol check. Will use mc_view (probably)"); } } checkedForJmol = true; @@ -1949,7 +1950,8 @@ public class JalviewLite extends Applet implements */ private void startLoading() { - dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile"); + dbgMsg("Loading thread started with:\n>>file\n" + _file + + ">>endfile"); dbgMsg("Loading started."); @@ -2050,14 +2052,14 @@ public class JalviewLite extends Applet implements if (protocol == DataSourceType.PASTE) { - newAlignFrame.setTitle(MessageManager.formatMessage( - "label.sequences_from", new Object[] { applet - .getDocumentBase().toString() })); + newAlignFrame.setTitle(MessageManager + .formatMessage("label.sequences_from", new Object[] + { applet.getDocumentBase().toString() })); } newAlignFrame.statusBar.setText(MessageManager.formatMessage( - "label.successfully_loaded_file", - new Object[] { resolvedFile })); + "label.successfully_loaded_file", new Object[] + { resolvedFile })); return newAlignFrame; } @@ -2080,8 +2082,8 @@ public class JalviewLite extends Applet implements dbgMsg(">>>Dump finished."); } catch (Exception e) { - System.err - .println("Exception when trying to dump the content of the file parameter."); + System.err.println( + "Exception when trying to dump the content of the file parameter."); e.printStackTrace(); } } @@ -2104,8 +2106,8 @@ public class JalviewLite extends Applet implements * related to JAL-434 */ - applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles", - false)); + applet.setAlignPdbStructures( + getDefaultParameter("alignpdbfiles", false)); /* * @@ -2121,9 +2123,11 @@ public class JalviewLite extends Applet implements Vector pdbs = new Vector(); // create a lazy matcher if we're asked to jalview.analysis.SequenceIdMatcher matcher = (applet - .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher( - alignFrame.getAlignViewport().getAlignment() - .getSequencesArray()) : null; + .getDefaultParameter("relaxedidmatch", false)) + ? new jalview.analysis.SequenceIdMatcher( + alignFrame.getAlignViewport().getAlignment() + .getSequencesArray()) + : null; String param; do @@ -2152,8 +2156,9 @@ public class JalviewLite extends Applet implements String sequence = applet.getParameter("PDBSEQ"); if (sequence != null) { - seqs = new SequenceI[] { matcher == null ? (Sequence) alignFrame - .getAlignViewport().getAlignment().findName(sequence) + seqs = new SequenceI[] { matcher == null + ? (Sequence) alignFrame.getAlignViewport() + .getAlignment().findName(sequence) : matcher.findIdMatch(sequence) }; } @@ -2161,8 +2166,8 @@ public class JalviewLite extends Applet implements else { param = st.nextToken(); - List tmp = new ArrayList(); - List tmp2 = new ArrayList(); + List tmp = new ArrayList<>(); + List tmp2 = new ArrayList<>(); while (st.hasMoreTokens()) { @@ -2174,9 +2179,10 @@ public class JalviewLite extends Applet implements tmp2.add(st2.nextToken()); seqstring = st2.nextToken(); } - tmp.add(matcher == null ? (Sequence) alignFrame - .getAlignViewport().getAlignment() - .findName(seqstring) : matcher.findIdMatch(seqstring)); + tmp.add(matcher == null + ? (Sequence) alignFrame.getAlignViewport() + .getAlignment().findName(seqstring) + : matcher.findIdMatch(seqstring)); } seqs = tmp.toArray(new SequenceI[tmp.size()]); @@ -2196,8 +2202,9 @@ public class JalviewLite extends Applet implements if (seqs[i] != null) { ((Sequence) seqs[i]).addPDBId(pdb); - StructureSelectionManager.getStructureSelectionManager( - applet).registerPDBEntry(pdb); + StructureSelectionManager + .getStructureSelectionManager(applet) + .registerPDBEntry(pdb); } else { @@ -2205,8 +2212,8 @@ public class JalviewLite extends Applet implements { // 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 " + System.err.println( + "Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence " + i + ")"); } } @@ -2232,7 +2239,8 @@ public class JalviewLite extends Applet implements 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++) + for (int pdbsi = 0, pdbsiSize = pdbs + .size(); pdbsi < pdbsiSize; pdbsi++) { Object[] o = (Object[]) pdbs.elementAt(pdbsi); pdb[pdbsi] = (PDBEntry) o[0]; @@ -2272,12 +2280,9 @@ public class JalviewLite extends Applet implements JnetAnnotationMaker.add_annotation(predictions, alignFrame.viewport.getAlignment(), 0, false); // false == do not add sequence profile from concise output - SequenceI repseq = alignFrame.viewport.getAlignment() - .getSequenceAt(0); - alignFrame.viewport.getAlignment().setSeqrep(repseq); - HiddenColumns cs = new HiddenColumns(); - cs.hideInsertionsFor(repseq); - alignFrame.viewport.getAlignment().setHiddenColumns(cs); + + alignFrame.viewport.getAlignment().setupJPredAlignment(); + alignFrame.alignPanel.fontChanged(); alignFrame.alignPanel.setScrollValues(0, 0); result = true; @@ -2313,8 +2318,8 @@ public class JalviewLite extends Applet implements } else { - System.err - .println("Annotations were not added from annotation file '" + System.err.println( + "Annotations were not added from annotation file '" + param + "'"); } } @@ -2385,14 +2390,14 @@ public class JalviewLite extends Applet implements { if (debug) { - System.err - .println("Attempting to load T-COFFEE score file from the scoreFile parameter"); + System.err.println( + "Attempting to load T-COFFEE score file from the scoreFile parameter"); } result = alignFrame.loadScoreFile(sScoreFile); if (!result) { - System.err - .println("Failed to parse T-COFFEE parameter as a valid score file ('" + System.err.println( + "Failed to parse T-COFFEE parameter as a valid score file ('" + sScoreFile + "')"); } } catch (Exception e) @@ -2489,8 +2494,8 @@ public class JalviewLite extends Applet implements { return initialAlignFrame; } - System.err - .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use."); + System.err.println( + "Implementation error: Jalview Applet API cannot work out which AlignFrame to use."); return null; } @@ -2568,8 +2573,8 @@ public class JalviewLite extends Applet implements } if (debug) { - System.err.println("Empty Array from '" + separator - + "' separated List"); + System.err.println( + "Empty Array from '" + separator + "' separated List"); } return null; } @@ -2611,16 +2616,16 @@ public class JalviewLite extends Applet implements } if (debug) { - System.err.println("Returning '" + separator - + "' separated List:\n"); + 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"); + System.err.println( + "Returning empty '" + separator + "' separated List\n"); } return "" + separator; } @@ -2633,8 +2638,8 @@ public class JalviewLite extends Applet implements @Override public String getFeatureGroups() { - String lst = arrayToSeparatorList(getDefaultTargetFrame() - .getFeatureGroups()); + String lst = arrayToSeparatorList( + getDefaultTargetFrame().getFeatureGroups()); return lst; } @@ -2660,8 +2665,8 @@ public class JalviewLite extends Applet implements @Override public String getFeatureGroupsOfState(boolean visible) { - return arrayToSeparatorList(getDefaultTargetFrame() - .getFeatureGroupsOfState(visible)); + return arrayToSeparatorList( + getDefaultTargetFrame().getFeatureGroupsOfState(visible)); } /* @@ -2795,9 +2800,9 @@ public class JalviewLite extends Applet implements // callInitCallback(); } - private Hashtable jshashes = new Hashtable(); + private Hashtable jshashes = new Hashtable<>(); - private Hashtable> jsmessages = new Hashtable>(); + private Hashtable> jsmessages = new Hashtable<>(); public void setJsMessageSet(String messageclass, String viewId, String[] colcommands) @@ -2805,7 +2810,7 @@ public class JalviewLite extends Applet implements Hashtable msgset = jsmessages.get(messageclass); if (msgset == null) { - msgset = new Hashtable(); + msgset = new Hashtable<>(); jsmessages.put(messageclass, msgset); } msgset.put(viewId, colcommands); @@ -2894,8 +2899,8 @@ public class JalviewLite extends Applet implements Color col = ColorUtils.parseColourString(colprop); if (col == null) { - System.err.println("Couldn't parse '" + colprop - + "' as a colour for " + colparam); + System.err.println("Couldn't parse '" + colprop + "' as a colour for " + + colparam); } return (col == null) ? defcolour : col; } @@ -2930,8 +2935,7 @@ public class JalviewLite extends Applet implements String codebase = localref.toString(); String localfile = localref.getFile(); resolvedPath = codebase.substring(0, - codebase.length() - localfile.length()) - + targetPath; + codebase.length() - localfile.length()) + targetPath; return resolvedPath; } @@ -2965,8 +2969,8 @@ public class JalviewLite extends Applet implements } if (debug) { - System.err.println("resolveUrlForLocalOrAbsolute returning " - + resolvedPath); + System.err.println( + "resolveUrlForLocalOrAbsolute returning " + resolvedPath); } return resolvedPath; } @@ -2988,17 +2992,15 @@ public class JalviewLite extends Applet implements // form valid URL // Should really use docbase, not codebase. URL prepend; - url = resolveUrlForLocalOrAbsolute( - url, - prepend = getDefaultParameter("resolvetocodebase", false) ? getCodeBase() + url = resolveUrlForLocalOrAbsolute(url, + prepend = getDefaultParameter("resolvetocodebase", false) + ? getCodeBase() : getDocumentBase()); if (debug) { - System.err - .println("Show url (prepended " - + prepend - + " - toggle resolvetocodebase if code/docbase resolution is wrong): " - + url); + System.err.println("Show url (prepended " + prepend + + " - toggle resolvetocodebase if code/docbase resolution is wrong): " + + url); } } else