X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;fp=src%2Fjalview%2Fbin%2FJalview.java;h=2cf6f37488552e2922d70cd48953d6fdc95de7e8;hb=4f4671d6ef1cb82d03fa9959f4e46d692babc1ef;hp=047356bf088457a818a3dcf09806da7db8a7eeeb;hpb=28b7316981ef2facee7fd064b3d429c7b5b583d7;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 047356b..2cf6f37 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -553,8 +553,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi parseArguments(aparser, true); } - private Object parseArguments(ArgsParser aparser, - boolean isStartup) + private Object parseArguments(ArgsParser aparser, boolean isStartup) { boolean isJS = Platform.isJS(); @@ -1321,6 +1320,17 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi JalviewApp app = new JalviewApp() { + // TODO BH 2019 + // + // These are methods that are in JalviewLite that various classes call + // but are not in JalviewLiteJsApi. Or, even if they are, other classes + // call + // them to JalviewLite directly. Some may not be necessary, but they have + // to + // be at least mentioned here, or the classes calling them should + // reference + // JalviewLite itself. + private boolean alignPDBStructures; // From JalviewLite; not implemented private Hashtable> jsmessages; @@ -1472,7 +1482,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi @Override public StructureSelectionManagerProvider getStructureSelectionManagerProvider() { - // TODO Auto-generated method stub + // TODO Q: what exactly is this? BH return null; } @@ -1489,8 +1499,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi ColumnSelection colsel, HiddenColumns hidden, SelectionSource source, Object alignFrame) { - // TODO Auto-generated method stub - return null; + return appLoader.getSelectionForListener(getCurrentAlignFrame(), + seqsel, colsel, hidden, source, alignFrame); } @Override @@ -1502,16 +1512,14 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi @Override public Hashtable getJSHashes() { - return (jshashes == null - ? (jshashes = new Hashtable<>()) + return (jshashes == null ? (jshashes = new Hashtable<>()) : jshashes); } @Override public Hashtable> getJSMessages() { - return (jsmessages == null - ? (jsmessages = new Hashtable<>()) + return (jsmessages == null ? (jsmessages = new Hashtable<>()) : jsmessages); } @@ -1602,11 +1610,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public void highlightIn(AlignFrameI alf, - String sequenceId, String position, String alignedPosition) + public void highlightIn(AlignFrameI alf, String sequenceId, + String position, String alignedPosition) { - appLoader.highlightIn(alf, sequenceId, position, - alignedPosition); + appLoader.highlightIn(alf, sequenceId, position, alignedPosition); } @Override @@ -1622,15 +1629,14 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public void selectIn(AlignFrameI alf, String sequenceIds, - String columns) + public void selectIn(AlignFrameI alf, String sequenceIds, String columns) { selectIn(alf, sequenceIds, columns, null); } @Override - public void selectIn(AlignFrameI alf, String sequenceIds, - String columns, String sep) + public void selectIn(AlignFrameI alf, String sequenceIds, String columns, + String sep) { appLoader.selectIn(alf, sequenceIds, columns, sep); } @@ -1644,8 +1650,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public String getSelectedSequencesAsAlignmentFrom( - AlignFrameI alf, String format, String sep) + public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf, + String format, String sep) { return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep); } @@ -1663,8 +1669,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public String getAlignmentOrderFrom(AlignFrameI alf, - String sep) + public String getAlignmentOrderFrom(AlignFrameI alf, String sep) { return appLoader.getAlignmentOrderFrom(alf, sep); } @@ -1682,8 +1687,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public String orderAlignmentBy(AlignFrameI alf, - String order, String undoName, String sep) + public String orderAlignmentBy(AlignFrameI alf, String order, + String undoName, String sep) { return appLoader.orderAlignmentBy(alf, order, undoName, sep); } @@ -1695,8 +1700,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public String getAlignmentFrom(AlignFrameI alf, - String format) + public String getAlignmentFrom(AlignFrameI alf, String format) { return getAlignmentFrom(alf, format, null); } @@ -1708,8 +1712,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public String getAlignmentFrom(AlignFrameI alf, - String format, String suffix) + public String getAlignmentFrom(AlignFrameI alf, String format, + String suffix) { return appLoader.getAlignmentFrom(alf, format, suffix); } @@ -1717,176 +1721,106 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi @Override public void loadAnnotation(String annotation) { - // TODO Auto-generated method stub - + loadAnnotationFrom(getCurrentAlignFrame(), annotation); } @Override - public void loadAnnotationFrom(AlignFrameI alf, - String annotation) + public void loadAnnotationFrom(AlignFrameI alf, String annotation) { - // TODO Auto-generated method stub - + appLoader.loadAnnotationFrom(alf, annotation); } @Override public void loadFeatures(String features, boolean autoenabledisplay) { - // TODO Auto-generated method stub - + loadFeaturesFrom(currentAlignFrame, features, autoenabledisplay); } @Override - public boolean loadFeaturesFrom(AlignFrameI alf, - String features, boolean autoenabledisplay) + public boolean loadFeaturesFrom(AlignFrameI alf, String features, + boolean autoenabledisplay) { - // TODO Auto-generated method stub - return false; + return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay); } @Override public String getFeatures(String format) { - // TODO Auto-generated method stub - return null; + return getFeaturesFrom(getCurrentAlignFrame(), format); } @Override - public String getFeaturesFrom(AlignFrameI alf, - String format) + public String getFeaturesFrom(AlignFrameI alf, String format) { - // TODO Auto-generated method stub - return null; + return appLoader.getFeaturesFrom(alf, format); } @Override public String getAnnotation() { - // TODO Auto-generated method stub - return null; + return getAnnotationFrom(getCurrentAlignFrame()); } @Override public String getAnnotationFrom(AlignFrameI alf) { - // TODO Auto-generated method stub - return null; + return appLoader.getAnnotationFrom(alf); } @Override public AlignFrameI newView() { - // TODO Auto-generated method stub - return null; + return newViewFrom(getCurrentAlignFrame(), null); } @Override public AlignFrameI newView(String name) { - // TODO Auto-generated method stub - return null; + return newViewFrom(getCurrentAlignFrame(), name); } @Override public AlignFrameI newViewFrom(AlignFrameI alf) { - // TODO Auto-generated method stub - return null; + return newViewFrom(alf, null); } @Override public AlignFrameI newViewFrom(AlignFrameI alf, String name) { - // TODO Auto-generated method stub - return null; + return appLoader.newViewFrom(alf, name); } @Override - public AlignFrameI loadAlignment(String text, - String title) + public AlignFrameI loadAlignment(String text, String title) { return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT, title); } @Override - public void setMouseoverListener(String listener) - { - // TODO Auto-generated method stub - - } - - @Override - public void setMouseoverListener(AlignFrameI af, - String listener) - { - // TODO Auto-generated method stub - - } - - @Override - public void setSelectionListener(String listener) - { - // TODO Auto-generated method stub - - } - - @Override - public void setSelectionListener(AlignFrameI af, - String listener) - { - // TODO Auto-generated method stub - - } - - @Override - public void setStructureListener(String listener, String modelSet) - { - // TODO Auto-generated method stub - - } - - @Override - public void removeJavascriptListener(AlignFrameI af, - String listener) - { - // TODO Auto-generated method stub - - } - - @Override - public void mouseOverStructure(String pdbResNum, String chain, - String pdbfile) - { - // TODO Auto-generated method stub - - } - - @Override - public boolean addPdbFile(AlignFrameI alFrame, - String sequenceId, String pdbEntryString, String pdbFile) + public boolean addPdbFile(AlignFrameI alFrame, String sequenceId, + String pdbEntryString, String pdbFile) { return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString, pdbFile); } @Override - public void scrollViewToIn(AlignFrameI alf, - String topRow, String leftHandColumn) + public void scrollViewToIn(AlignFrameI alf, String topRow, + String leftHandColumn) { appLoader.scrollViewToIn(alf, topRow, leftHandColumn); } @Override - public void scrollViewToRowIn(AlignFrameI alf, - String topRow) + public void scrollViewToRowIn(AlignFrameI alf, String topRow) { appLoader.scrollViewToRowIn(alf, topRow); } @Override - public void scrollViewToColumnIn(AlignFrameI alf, - String leftHandColumn) + public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn) { appLoader.scrollViewToColumnIn(alf, leftHandColumn); } @@ -1910,15 +1844,14 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public String getFeatureGroupsOfStateOn(AlignFrameI alf, - boolean visible) + public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible) { return appLoader.getFeatureGroupsOfStateOn(alf, visible); } @Override - public void setFeatureGroupStateOn(AlignFrameI alf, - String groups, boolean state) + public void setFeatureGroupStateOn(AlignFrameI alf, String groups, + boolean state) { setFeatureGroupStateOn(alf, groups, state); } @@ -1980,4 +1913,85 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi return CalculationChooser.openPcaPanel(af, modelName, null); } + @Override + public String getSelectedSequencesAsAlignment(String format, + boolean suffix) + { + return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(), + format, suffix); + } + + @Override + public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf, + String format, boolean suffix) + { + return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, + "" + suffix); + } + + @Override + public String arrayToSeparatorList(String[] array) + { + return appLoader.arrayToSeparatorList(array); + } + + @Override + public String[] separatorListToArray(String list) + { + return appLoader.separatorListToArray(list); + } + + //// probably not needed in JalviewJS -- From when Jmol and Jalview did not + //// have a direct connection? + + @Override + public void setMouseoverListener(String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void setMouseoverListener(AlignFrameI af, String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void setSelectionListener(String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void setSelectionListener(AlignFrameI af, String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void setStructureListener(String listener, String modelSet) + { + // TODO Auto-generated method stub + + } + + @Override + public void removeJavascriptListener(AlignFrameI af, String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void mouseOverStructure(String pdbResNum, String chain, + String pdbfile) + { + // TODO Auto-generated method stub + + } + }