X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewAppLoader.java;fp=src%2Fjalview%2Fbin%2FJalviewAppLoader.java;h=a7c504248b69cdef961afd649924aea414c10f99;hb=8bdcb5fb1d1fc9fccd8c6c97a17eb3ee4ceaa4d0;hp=51a03306e46382c3ac1221666481852f98dacdf0;hpb=25e36b8f366dab01f838d8175e59e9148628eb68;p=jalview.git diff --git a/src/jalview/bin/JalviewAppLoader.java b/src/jalview/bin/JalviewAppLoader.java index 51a0330..a7c5042 100644 --- a/src/jalview/bin/JalviewAppLoader.java +++ b/src/jalview/bin/JalviewAppLoader.java @@ -1,6 +1,5 @@ package jalview.bin; -import jalview.api.AlignFrameI; import jalview.api.JalviewApp; import jalview.api.StructureSelectionManagerProvider; import jalview.datamodel.Alignment; @@ -761,14 +760,14 @@ public class JalviewAppLoader return arrayToSeparatorList(array, separator); } - public String getSelectedSequencesFrom(AlignFrameI alf, String sep) + public String getSelectedSequencesFrom(AlignFrame alf, String sep) { StringBuffer result = new StringBuffer(""); if (sep == null || sep.length() == 0) { sep = separator; // "+0x00AC; } - AlignViewport v = ((AlignFrame) alf).getViewport(); + AlignViewport v = alf.getViewport(); if (v.getSelectionGroup() != null) { SequenceI[] seqs = v.getSelectionGroup() @@ -784,7 +783,7 @@ public class JalviewAppLoader return result.toString(); } - public void setFeatureGroupStateOn(final AlignFrameI alf, + public void setFeatureGroupStateOn(final AlignFrame alf, final String groups, boolean state) { java.awt.EventQueue.invokeLater(new Runnable() @@ -792,19 +791,19 @@ public class JalviewAppLoader @Override public void run() { - ((AlignFrame) alf).setFeatureGroupState( + alf.setFeatureGroupState( separatorListToArray(groups, separator), state); } }); } - public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible) + public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible) { return arrayToSeparatorList( - ((AlignFrame) alf).getFeatureGroupsOfState(visible)); + alf.getFeatureGroupsOfState(visible)); } - public void scrollViewToIn(final AlignFrameI alf, final String topRow, + public void scrollViewToIn(final AlignFrame alf, final String topRow, final String leftHandColumn) { java.awt.EventQueue.invokeLater(new Runnable() @@ -814,8 +813,8 @@ public class JalviewAppLoader { try { - ((AlignFrame) alf).scrollTo(new Integer(topRow).intValue(), - new Integer(leftHandColumn).intValue()); + alf.scrollTo(Integer.valueOf(topRow).intValue(), + Integer.valueOf(leftHandColumn).intValue()); } catch (Exception ex) { @@ -828,7 +827,7 @@ public class JalviewAppLoader }); } - public void scrollViewToRowIn(final AlignFrameI alf, final String topRow) + public void scrollViewToRowIn(final AlignFrame alf, final String topRow) { java.awt.EventQueue.invokeLater(new Runnable() @@ -838,7 +837,7 @@ public class JalviewAppLoader { try { - ((AlignFrame) alf).scrollToRow(new Integer(topRow).intValue()); + alf.scrollToRow(Integer.valueOf(topRow).intValue()); } catch (Exception ex) { @@ -851,7 +850,7 @@ public class JalviewAppLoader }); } - public void scrollViewToColumnIn(final AlignFrameI alf, + public void scrollViewToColumnIn(final AlignFrame alf, final String leftHandColumn) { java.awt.EventQueue.invokeLater(new Runnable() @@ -862,8 +861,9 @@ public class JalviewAppLoader { try { - ((AlignFrame) alf) - .scrollToColumn(new Integer(leftHandColumn).intValue()); + alf + .scrollToColumn( + Integer.valueOf(leftHandColumn).intValue()); } catch (Exception ex) { @@ -877,10 +877,10 @@ public class JalviewAppLoader } - public boolean addPdbFile(AlignFrameI alf, String sequenceId, + public boolean addPdbFile(AlignFrame alf, String sequenceId, String pdbEntryString, String pdbFile) { - AlignFrame alFrame = (AlignFrame) alf; + AlignFrame alFrame = alf; SequenceI toaddpdb = alFrame.getViewport().getAlignment() .findName(sequenceId); boolean needtoadd = false; @@ -930,7 +930,7 @@ public class JalviewAppLoader return true; } - public AlignFrameI loadAlignment(String text, int width, int height, + public AlignFrame loadAlignment(String text, int width, int height, String title) { AlignmentI al = null; @@ -952,18 +952,18 @@ public class JalviewAppLoader return null; } - public String getFeatureGroupsOn(AlignFrameI alf) + public String getFeatureGroupsOn(AlignFrame alf) { return arrayToSeparatorList( - ((AlignFrame) alf).getFeatureGroups()); + alf.getFeatureGroups()); } - public void highlightIn(final AlignFrameI alf, final String sequenceId, + public void highlightIn(final AlignFrame alf, final String sequenceId, final String position, final String alignedPosition) { // TODO: could try to highlight in all alignments if alf==null jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher( - ((AlignFrame) alf).getViewport().getAlignment() + alf.getViewport().getAlignment() .getSequencesArray()); final SequenceI sq = matcher.findIdMatch(sequenceId); if (sq != null) @@ -971,7 +971,7 @@ public class JalviewAppLoader int apos = -1; try { - apos = new Integer(position).intValue(); + apos = Integer.valueOf(position).intValue(); apos--; } catch (NumberFormatException ex) { @@ -1009,7 +1009,7 @@ public class JalviewAppLoader } } - public void selectIn(final AlignFrameI alf, String sequenceIds, + public void selectIn(final AlignFrame alf, String sequenceIds, String columns, String sep) { if (sep == null || sep.length() == 0) @@ -1029,9 +1029,9 @@ public class JalviewAppLoader String[] cols = JalviewAppLoader.separatorListToArray(columns, sep); final SequenceGroup sel = new SequenceGroup(); final ColumnSelection csel = new ColumnSelection(); - AlignmentI al = ((AlignFrame) alf).getViewport().getAlignment(); + AlignmentI al = alf.getViewport().getAlignment(); jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher( - ((AlignFrame) alf).getViewport().getAlignment() + alf.getViewport().getAlignment() .getSequencesArray()); int start = 0, end = al.getWidth(), alw = al.getWidth(); boolean seqsfound = true; @@ -1069,7 +1069,7 @@ public class JalviewAppLoader 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) { @@ -1080,7 +1080,7 @@ public class JalviewAppLoader } try { - to = new Integer(cl.substring(p + 1)).intValue(); + to = Integer.valueOf(cl.substring(p + 1)).intValue(); to--; } catch (NumberFormatException ex) { @@ -1140,7 +1140,7 @@ public class JalviewAppLoader int r = -1; try { - r = new Integer(cl).intValue(); + r = Integer.valueOf(cl).intValue(); r--; } catch (NumberFormatException ex) { @@ -1216,16 +1216,16 @@ public class JalviewAppLoader @Override public void run() { - ((AlignFrame) alf).select(sel, csel, ((AlignFrame) alf) + alf.select(sel, csel, alf .getCurrentView().getAlignment().getHiddenColumns()); } }); } } - public String getAlignmentOrderFrom(AlignFrameI alf, String sep) + public String getAlignmentOrderFrom(AlignFrame alf, String sep) { - AlignmentI alorder = ((AlignFrame) alf).getViewport().getAlignment(); + AlignmentI alorder = alf.getViewport().getAlignment(); String[] order = new String[alorder.getHeight()]; for (int i = 0; i < order.length; i++) { @@ -1234,12 +1234,12 @@ public class JalviewAppLoader return arrayToSeparatorList(order, sep); } - public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf, + public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, String suffix) { try { - AlignViewport vp = ((AlignFrame) alf).getViewport(); + AlignViewport vp = alf.getViewport(); FileFormatI theFormat = FileFormats.getInstance().forName(format); boolean seqlimits = (suffix == null || suffix.equalsIgnoreCase("true")); @@ -1262,7 +1262,7 @@ public class JalviewAppLoader return ""; } - public String orderAlignmentBy(AlignFrameI alf, String order, + public String orderAlignmentBy(AlignFrame alf, String order, String undoName, String sep) { if (sep == null || sep.length() == 0) @@ -1274,7 +1274,7 @@ public class JalviewAppLoader if (ids != null && ids.length > 0) { jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher( - ((AlignFrame) alf).getViewport().getAlignment() + alf.getViewport().getAlignment() .getSequencesArray()); int s = 0; sqs = new SequenceI[ids.length]; @@ -1315,10 +1315,10 @@ public class JalviewAppLoader final String _undoName = undoName; // TODO: deal with synchronization here: cannot raise any events until after // this has returned. - return ((AlignFrame) alf).sortBy(aorder, _undoName) ? "true" : ""; + return alf.sortBy(aorder, _undoName) ? "true" : ""; } - public String getAlignmentFrom(AlignFrameI alf, String format, + public String getAlignmentFrom(AlignFrame alf, String format, String suffix) { try @@ -1328,7 +1328,7 @@ public class JalviewAppLoader FileFormatI theFormat = FileFormats.getInstance().forName(format); String reply = new AppletFormatAdapter().formatSequences(theFormat, - ((AlignFrame) alf).getViewport().getAlignment(), seqlimits); + alf.getViewport().getAlignment(), seqlimits); return reply; } catch (IllegalArgumentException ex) { @@ -1338,26 +1338,26 @@ public class JalviewAppLoader } } - public void loadAnnotationFrom(AlignFrameI alf, String annotation) + public void loadAnnotationFrom(AlignFrame alf, String annotation) { if (new AnnotationFile().annotateAlignmentView( - ((AlignFrame) alf).getViewport(), annotation, + alf.getViewport(), annotation, DataSourceType.PASTE)) { - ((AlignFrame) alf).alignPanel.fontChanged(); - ((AlignFrame) alf).alignPanel.setScrollValues(0, 0); + alf.alignPanel.fontChanged(); + alf.alignPanel.setScrollValues(0, 0); } else { - ((AlignFrame) alf).parseFeaturesFile(annotation, + alf.parseFeaturesFile(annotation, DataSourceType.PASTE); } } - public boolean loadFeaturesFrom(AlignFrameI alf, String features, + public boolean loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay) { - boolean ret = ((AlignFrame) alf).parseFeaturesFile(features, + boolean ret = alf.parseFeaturesFile(features, DataSourceType.PASTE); if (!ret) { @@ -1365,16 +1365,16 @@ public class JalviewAppLoader } if (autoenabledisplay) { - ((AlignFrame) alf).getViewport().setShowSequenceFeatures(true); + alf.getViewport().setShowSequenceFeatures(true); // this next was for a checkbox in JalviewLite // ((AlignFrame) alf).getViewport().sequenceFeatures.setState(true); } return true; } - public String getFeaturesFrom(AlignFrameI alf, String format) + public String getFeaturesFrom(AlignFrame alf, String format) { - AlignFrame f = ((AlignFrame) alf); + AlignFrame f = (alf); String features; FeaturesFile formatter = new FeaturesFile(); @@ -1399,25 +1399,25 @@ public class JalviewAppLoader } - public String getAnnotationFrom(AlignFrameI alf) + public String getAnnotationFrom(AlignFrame alf) { - AlignFrame f = (AlignFrame) alf; + AlignFrame f = alf; String annotation = new AnnotationFile() .printAnnotationsForView(f.getViewport()); return annotation; } - public AlignFrameI newViewFrom(AlignFrameI alf, String name) - { - return (AlignFrameI) ((AlignFrame) alf).newView(name, true); - } - + // public AlignFrame newViewFrom(AlignFrame alf, String name) + // { + // return (AlignFrame) alf.newView(name, true); + // } + // public String[] separatorListToArray(String list) { return separatorListToArray(list, separator); } - public Object[] getSelectionForListener(AlignFrameI currentFrame, + public Object[] getSelectionForListener(AlignFrame currentFrame, SequenceGroup seqsel, ColumnSelection colsel, HiddenColumns hidden, SelectionSource source, Object alignFrame) { @@ -1428,10 +1428,10 @@ public class JalviewAppLoader if (source != null) { if (source instanceof AlignViewport - && ((AlignFrame) currentFrame).getViewport() == source) + && currentFrame.getViewport() == source) { // should be valid if it just generated an event! - src = (AlignFrame) currentFrame; + src = currentFrame; } }