X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=7d66f6d9997df9376d595679eaa0d9a127d8593a;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=de011ea45fcabb9e037f5ca8ab77ebf2e7835d7c;hpb=cd4e2687751aab1c9c5974e6966e610a3332236b;p=jalview.git diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index de011ea..7d66f6d 100644 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -20,6 +20,8 @@ */ package jalview.bin; +import java.util.Locale; + import jalview.analysis.AlignmentUtils; import jalview.api.StructureSelectionManagerProvider; import jalview.appletgui.AlignFrame; @@ -38,8 +40,8 @@ import jalview.datamodel.SequenceI; import jalview.io.AnnotationFile; import jalview.io.AppletFormatAdapter; import jalview.io.DataSourceType; -import jalview.io.FileFormat; import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.FileParse; import jalview.io.IdentifyFile; import jalview.io.JPredFile; @@ -51,6 +53,7 @@ import jalview.javascript.JsCallBack; import jalview.javascript.MouseOverStructureListener; import jalview.structure.SelectionListener; import jalview.structure.StructureSelectionManager; +import jalview.util.ColorUtils; import jalview.util.HttpUtils; import jalview.util.MessageManager; @@ -83,8 +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"; @@ -197,7 +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) { @@ -208,7 +211,7 @@ public class JalviewLite extends Applet implements // use vamsas listener to broadcast to all listeners in scope if (alignedPosition != null && (alignedPosition.trim().length() == 0 || alignedPosition - .toLowerCase().indexOf("false") > -1)) + .toLowerCase(Locale.ROOT).indexOf("false") > -1)) { java.awt.EventQueue.invokeLater(new Runnable() { @@ -337,23 +340,23 @@ 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; } @@ -408,19 +411,19 @@ public class JalviewLite extends Applet implements int r = -1; try { - r = new Integer(cl).intValue(); + r = Integer.valueOf(cl).intValue(); r--; } catch (NumberFormatException ex) { - if (cl.toLowerCase().equals("sequence")) + if (cl.toLowerCase(Locale.ROOT).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 '" + System.err.println( + "ERROR: Couldn't parse integer from point selection element of column selection string '" + cl + "'"); return; } @@ -470,7 +473,7 @@ 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) { @@ -484,7 +487,8 @@ public class JalviewLite extends Applet implements @Override public void run() { - alf.select(sel, csel); + alf.select(sel, csel, + alf.getAlignViewport().getAlignment().getHiddenColumns()); } }); } @@ -498,7 +502,8 @@ 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); @@ -517,7 +522,7 @@ public class JalviewLite extends Applet implements { try { - FileFormatI theFormat = FileFormat.valueOf(format); + FileFormatI theFormat = FileFormats.getInstance().forName(format); boolean seqlimits = suffix.equalsIgnoreCase(TRUE); if (alf.viewport.getSelectionGroup() != null) { @@ -715,7 +720,7 @@ public class JalviewLite extends Applet implements { boolean seqlimits = suffix.equalsIgnoreCase(TRUE); - FileFormatI theFormat = FileFormat.valueOf(format); + FileFormatI theFormat = FileFormats.getInstance().forName(format); String reply = new AppletFormatAdapter().formatSequences(theFormat, alf.viewport.getAlignment(), seqlimits); return reply; @@ -918,7 +923,7 @@ public class JalviewLite extends Applet implements setMouseoverListener(currentAlignFrame, listener); } - private Vector javascriptListeners = new Vector(); + private Vector javascriptListeners = new Vector<>(); /* * (non-Javadoc) @@ -935,8 +940,8 @@ 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; } } @@ -948,8 +953,9 @@ 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."); } @@ -981,8 +987,8 @@ 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; } } @@ -994,8 +1000,9 @@ 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."); } @@ -1020,8 +1027,8 @@ 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; } } @@ -1062,9 +1069,8 @@ 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--; @@ -1161,8 +1167,8 @@ 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() @@ -1173,13 +1179,13 @@ 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) { @@ -1209,8 +1215,8 @@ 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) { @@ -1241,7 +1247,7 @@ public class JalviewLite extends Applet implements { try { - alf.scrollToRow(new Integer(topRow).intValue()); + alf.scrollToRow(Integer.valueOf(topRow).intValue()); } catch (Exception ex) { @@ -1273,12 +1279,12 @@ 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(); } @@ -1330,7 +1336,7 @@ 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; @@ -1352,8 +1358,8 @@ 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) { @@ -1420,8 +1426,8 @@ 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(); @@ -1437,7 +1443,8 @@ public class JalviewLite extends Applet implements String externalsviewer = getParameter("externalstructureviewer"); if (externalsviewer != null) { - useXtrnalSviewer = externalsviewer.trim().toLowerCase().equals(TRUE); + useXtrnalSviewer = externalsviewer.trim().toLowerCase(Locale.ROOT) + .equals(TRUE); } /** * if true disable the check for jmol @@ -1463,9 +1470,8 @@ 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; @@ -1622,8 +1628,8 @@ 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 '" @@ -1734,8 +1740,8 @@ 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) @@ -1795,8 +1801,8 @@ 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) { @@ -1807,8 +1813,8 @@ 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; @@ -1946,7 +1952,8 @@ 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."); @@ -2047,14 +2054,14 @@ 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; } @@ -2077,8 +2084,8 @@ 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(); } } @@ -2101,8 +2108,8 @@ public class JalviewLite extends Applet implements * related to JAL-434 */ - applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles", - false)); + applet.setAlignPdbStructures( + getDefaultParameter("alignpdbfiles", false)); /* * @@ -2118,9 +2125,11 @@ 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 @@ -2149,8 +2158,9 @@ 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) }; } @@ -2158,8 +2168,8 @@ 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()) { @@ -2171,9 +2181,10 @@ 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()]); @@ -2193,8 +2204,9 @@ 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 { @@ -2202,8 +2214,8 @@ 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 + ")"); } } @@ -2229,7 +2241,8 @@ 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]; @@ -2269,12 +2282,9 @@ 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); - ColumnSelection cs = new ColumnSelection(); - cs.hideInsertionsFor(repseq); - alignFrame.viewport.setColumnSelection(cs); + + alignFrame.viewport.getAlignment().setupJPredAlignment(); + alignFrame.alignPanel.fontChanged(); alignFrame.alignPanel.setScrollValues(0, 0); result = true; @@ -2310,8 +2320,8 @@ 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 + "'"); } } @@ -2382,14 +2392,14 @@ 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) @@ -2486,8 +2496,8 @@ 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; } @@ -2565,8 +2575,8 @@ 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; } @@ -2608,16 +2618,16 @@ 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; } @@ -2630,8 +2640,8 @@ public class JalviewLite extends Applet implements @Override public String getFeatureGroups() { - String lst = arrayToSeparatorList(getDefaultTargetFrame() - .getFeatureGroups()); + String lst = arrayToSeparatorList( + getDefaultTargetFrame().getFeatureGroups()); return lst; } @@ -2657,8 +2667,8 @@ public class JalviewLite extends Applet implements @Override public String getFeatureGroupsOfState(boolean visible) { - return arrayToSeparatorList(getDefaultTargetFrame() - .getFeatureGroupsOfState(visible)); + return arrayToSeparatorList( + getDefaultTargetFrame().getFeatureGroupsOfState(visible)); } /* @@ -2685,7 +2695,7 @@ public class JalviewLite extends Applet implements final String groups, boolean state) { final boolean st = state;// !(state==null || state.equals("") || - // state.toLowerCase().equals("false")); + // state.toLowerCase(Locale.ROOT).equals("false")); java.awt.EventQueue.invokeLater(new Runnable() { @Override @@ -2792,9 +2802,9 @@ 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) @@ -2802,7 +2812,7 @@ 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); @@ -2888,22 +2898,13 @@ public class JalviewLite extends Applet implements { return defcolour; } - Color col = jalview.schemes.ColourSchemeProperty - .getAWTColorFromName(colprop); + Color col = ColorUtils.parseColourString(colprop); if (col == null) { - try - { - col = new jalview.schemes.UserColourScheme(colprop).findColour('A'); - } catch (Exception ex) - { - System.err.println("Couldn't parse '" + colprop - + "' as a colour for " + colparam); - col = null; - } + System.err.println("Couldn't parse '" + colprop + "' as a colour for " + + colparam); } return (col == null) ? defcolour : col; - } public void openJalviewHelpUrl() @@ -2936,8 +2937,7 @@ 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; } @@ -2971,8 +2971,8 @@ public class JalviewLite extends Applet implements } if (debug) { - System.err.println("resolveUrlForLocalOrAbsolute returning " - + resolvedPath); + System.err.println( + "resolveUrlForLocalOrAbsolute returning " + resolvedPath); } return resolvedPath; } @@ -2994,17 +2994,15 @@ 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