X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=d79184242a80a5cafdb1703168e159c40f640450;hb=a6152ff382c65a2cbd95163478cce7a65b1c641a;hp=61ee23161086cc9d674ffc585f02640ea9a144b2;hpb=dc24bc768061f6e08be77d7e18709da98c6f9428;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 61ee231..d791842 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -20,6 +20,8 @@ */ package jalview.gui; +import java.util.Locale; + import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; @@ -91,6 +93,7 @@ import jalview.api.SplitContainerI; import jalview.api.ViewStyleI; import jalview.api.analysis.SimilarityParamsI; import jalview.bin.Cache; +import jalview.bin.Console; import jalview.bin.Jalview; import jalview.commands.CommandI; import jalview.commands.EditCommand; @@ -366,7 +369,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // modifyPID.setEnabled(false); } - String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", + String sortby = Cache.getDefault("SORT_ALIGNMENT", "No sort"); if (sortby.equals("Id")) @@ -409,7 +412,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, wrapMenuItem_actionPerformed(null); } - if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false)) + if (Cache.getDefault("SHOW_OVERVIEW", false)) { this.overviewMenuItem_actionPerformed(null); } @@ -484,9 +487,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } }); - if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase() + if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT) .indexOf("devel") > -1 - || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase() + || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT) .indexOf("test") > -1) { formatMenu.add(vsel); @@ -565,7 +568,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.getSeqPanel().moveCursor(0, 1); + alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown()); } break; @@ -576,7 +579,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.getSeqPanel().moveCursor(0, -1); + alignPanel.getSeqPanel().moveCursor(0, -1,evt.isShiftDown()); } break; @@ -589,7 +592,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.getSeqPanel().moveCursor(-1, 0); + alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown()); } break; @@ -601,7 +604,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.getSeqPanel().moveCursor(1, 0); + alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown()); } break; @@ -1012,7 +1015,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public String getVersion() { - return jalview.bin.Cache.getProperty("VERSION"); + return Cache.getProperty("VERSION"); } public FeatureRenderer getFeatureRenderer() @@ -1214,7 +1217,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - Cache.log.error(MessageManager + Console.error(MessageManager .formatMessage("label.couldnt_save_file", new Object[] { lastFilenameSaved })); } @@ -1297,7 +1300,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, BackupFiles backupfiles = null; if (doBackup) { - Cache.log.trace( + Console.trace( "ALIGNFRAME making backupfiles object for " + file); backupfiles = new BackupFiles(file); } @@ -1305,19 +1308,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file; - Cache.log.trace("ALIGNFRAME setting PrintWriter"); + Console.trace("ALIGNFRAME setting PrintWriter"); PrintWriter out = new PrintWriter(new FileWriter(tempFilePath)); if (backupfiles != null) { - Cache.log.trace("ALIGNFRAME about to write to temp file " + Console.trace("ALIGNFRAME about to write to temp file " + backupfiles.getTempFilePath()); } out.print(output); - Cache.log.trace("ALIGNFRAME about to close file"); + Console.trace("ALIGNFRAME about to close file"); out.close(); - Cache.log.trace("ALIGNFRAME closed file"); + Console.trace("ALIGNFRAME closed file"); AlignFrame.this.setTitle(file); statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", @@ -1327,29 +1330,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (IOException e) { lastSaveSuccessful = false; - Cache.log.error( + Console.error( "ALIGNFRAME Something happened writing the temp file"); - Cache.log.error(e.getMessage()); - Cache.log.debug(Cache.getStackTraceString(e)); + Console.error(e.getMessage()); + Console.debug(Cache.getStackTraceString(e)); } catch (Exception ex) { lastSaveSuccessful = false; - Cache.log.error( + Console.error( "ALIGNFRAME Something unexpected happened writing the temp file"); - Cache.log.error(ex.getMessage()); - Cache.log.debug(Cache.getStackTraceString(ex)); + Console.error(ex.getMessage()); + Console.debug(Cache.getStackTraceString(ex)); } if (doBackup) { backupfiles.setWriteSuccess(lastSaveSuccessful); - Cache.log.debug("ALIGNFRAME writing temp file was " + Console.debug("ALIGNFRAME writing temp file was " + (lastSaveSuccessful ? "" : "NOT ") + "successful"); // do the backup file roll and rename the temp file to actual file - Cache.log.trace( + Console.trace( "ALIGNFRAME about to rollBackupsAndRenameTempFile"); lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile(); - Cache.log.debug( + Console.debug( "ALIGNFRAME performed rollBackupsAndRenameTempFile " + (lastSaveSuccessful ? "" : "un") + "successfully"); @@ -1532,7 +1535,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void associatedData_actionPerformed(ActionEvent e) { final JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); String tooltip = MessageManager .getString("label.load_jalview_annotations"); @@ -1544,7 +1547,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void run() { String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + Cache.setProperty("LAST_DIRECTORY", choice); loadJalviewDataFile(chooser.getSelectedFile(), null, null, null); } }); @@ -1731,7 +1734,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (originalSource != viewport) { - Cache.log.warn( + Console.warn( "Implementation worry: mismatch of viewport origin for undo"); } originalSource.updateHiddenColumns(); @@ -1771,7 +1774,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (originalSource != viewport) { - Cache.log.warn( + Console.warn( "Implementation worry: mismatch of viewport origin for redo"); } originalSource.updateHiddenColumns(); @@ -4067,7 +4070,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // Pick the tree file JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.select_newick_like_tree_file")); @@ -4286,9 +4289,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, webService.add(me.webServiceNoServices); } // TODO: move into separate menu builder class. - boolean new_sspred = false; - if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { + // logic for 2.11.1.4 is + // always look to see if there is a discover. if there isn't + // we can't show any Jws2 services + // if there are services available, show them - regardless of + // the 'show JWS2 preference' + // if the discoverer is running then say so + // otherwise offer to trigger discovery if 'show JWS2' is not + // enabled Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer(); if (jws2servs != null) { @@ -4297,7 +4306,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, jws2servs.attachWSMenuEntry(webService, me); for (Jws2Instance sv : jws2servs.getServices()) { - if (sv.description.toLowerCase().contains("jpred")) + if (sv.description.toLowerCase(Locale.ROOT).contains("jpred")) { for (JMenuItem jmi : legacyItems) { @@ -4305,8 +4314,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } } - } + if (jws2servs.isRunning()) { JMenuItem tm = new JMenuItem( @@ -4314,6 +4323,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, tm.setEnabled(false); webService.add(tm); } + else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true)) + { + JMenuItem enableJws2 = new JMenuItem( + "Discover Web Services"); + enableJws2.setToolTipText( + "Select to start JABA Web Service discovery (or enable option in Web Service preferences)"); + enableJws2.setEnabled(true); + enableJws2.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + // start service discoverer, but ignore preference + Desktop.instance.startServiceDiscovery(false, + true); + } + }); + webService.add(enableJws2); + } } } build_urlServiceMenu(me.webService); @@ -4331,7 +4360,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } catch (Exception e) { - Cache.log.debug( + Console.debug( "Exception during web service menu building process.", e); } @@ -4428,7 +4457,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showProducts.setEnabled(showp); } catch (Exception e) { - Cache.log.warn( + Console.warn( "canShowProducts threw an exception - please report to help@jalview.org", e); return false; @@ -4469,7 +4498,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, al = dna.translateCdna(codeTable); } catch (Exception ex) { - jalview.bin.Cache.log.error( + Console.error( "Exception during translation. Please report this !", ex); final String msg = MessageManager.getString( "label.error_when_translating_sequences_submit_bug_report"); @@ -4832,7 +4861,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } catch (Exception x) { - Cache.log.debug( + Console.debug( "Exception when processing data source as T-COFFEE score file", x); tcf = null;