X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=7b1dfeb10c4a81e1b87b0a7390eeb5a3ac5f81b4;hb=c858b2b71816055429bd496a7158973ad8acec57;hp=48758cda957fce722679cef4130b9de62a506cc1;hpb=ed8d18abc302ac802ad1d0611f3fe2fef570ab5e;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 48758cd..7b1dfeb 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -310,7 +310,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener SequenceGroup sg = viewport.getSelectionGroup(); if (toggleSeqs) { - if (sg != null && sg.getSize(false) != viewport.alignment.getHeight()) + if (sg != null && sg.getSize() != viewport.alignment.getHeight()) { hideSelSequences_actionPerformed(null); hide = true; @@ -825,6 +825,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener alignPanel.makeEPS(f); } + + public void pageSetup_actionPerformed(ActionEvent e) + { + PrinterJob printJob = PrinterJob.getPrinterJob(); + PrintThread.pf = printJob.pageDialog(printJob.defaultPage()); + } + /** * DOCUMENT ME! * @@ -833,7 +840,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener public void printMenuItem_actionPerformed(ActionEvent e) { //Putting in a thread avoids Swing painting problems - PrintThread thread = new PrintThread(); + PrintThread thread = new PrintThread(alignPanel); thread.start(); } @@ -1082,14 +1089,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.getSequences(false).contains(seq)) + if (!sg.getSequences(null).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (sg.getSequences(false).contains(temp)) + if (sg.getSequences(null).contains(temp)) { continue; } @@ -1104,14 +1111,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.getSequences(false).contains(seq)) + if (!sg.getSequences(null).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (sg.getSequences(false).contains(temp)) + if (sg.getSequences(null).contains(temp)) { continue; } @@ -1156,6 +1163,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener try { + jalview.gui.Desktop.internalCopy = true; //Its really worth setting the clipboard contents //to empty before setting the large StringSelection!! Toolkit.getDefaultToolkit().getSystemClipboard() @@ -1435,7 +1443,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener Vector seqs = new Vector(); SequenceI seq; - for (int i = 0; i < sg.getSize(false); i++) + for (int i = 0; i < sg.getSize(); i++) { seq = sg.getSequenceAt(i); seqs.addElement(seq); @@ -1443,7 +1451,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener // If the cut affects all sequences, remove highlighted columns - if (sg.getSize(false) == viewport.alignment.getHeight()) + if (sg.getSize() == viewport.alignment.getHeight()) { viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes() + 1); @@ -1608,7 +1616,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener SequenceI [] seqs; if(viewport.getSelectionGroup()!=null) - seqs = viewport.getSelectionGroup().getSequencesAsArray(true); + seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences); else seqs = viewport.alignment.getSequencesArray(); @@ -1671,7 +1679,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray(true); + seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } @@ -1683,7 +1691,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener new RemoveGapColCommand("Remove Gapped Columns", seqs, start, end, - viewport.getGapCharacter()); + viewport.alignment); addHistoryItem(removeGapCols); @@ -1715,7 +1723,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray(true); + seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } @@ -1728,9 +1736,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener int startRes = seq.findPosition(viewport.startRes); addHistoryItem(new RemoveGapsCommand("Remove Gaps", - seqs, - start, end, - viewport.getGapCharacter())); + seqs, + start, end, + viewport.alignment)); viewport.setStartRes(seq.findIndex(startRes)-1); @@ -2230,7 +2238,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener if (cs instanceof ClustalxColourScheme) { sg.cs = new ClustalxColourScheme( - sg.getSequences(true), sg.getWidth()); + sg.getSequences(viewport.hiddenRepSequences), sg.getWidth()); } else if (cs instanceof UserColourScheme) { @@ -2255,7 +2263,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener viewport.getIgnoreGapsConsensus()); sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(true), sg.getStartRes(), + sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(), sg.getEndRes()+1)); } else @@ -2266,7 +2274,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener { Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, - sg.getSequences(true), + sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(), sg.getEndRes()+1); c.calculate(); @@ -2518,7 +2526,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { if ( (viewport.getSelectionGroup() == null) || - (viewport.getSelectionGroup().getSize(false) < 2)) + (viewport.getSelectionGroup().getSize() < 2)) { JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", @@ -2541,8 +2549,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener public void PCAMenuItem_actionPerformed(ActionEvent e) { if ( ( (viewport.getSelectionGroup() != null) && - (viewport.getSelectionGroup().getSize(false) < 4) && - (viewport.getSelectionGroup().getSize(false) > 0)) || + (viewport.getSelectionGroup().getSize() < 4) && + (viewport.getSelectionGroup().getSize() > 0)) || (viewport.getAlignment().getHeight() < 4)) { JOptionPane.showInternalMessageDialog(this, @@ -2622,7 +2630,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener TreePanel tp; if (viewport.getSelectionGroup() != null) { - if (viewport.getSelectionGroup().getSize(false) < 3) { + if (viewport.getSelectionGroup().getSize() < 3) { JOptionPane.showMessageDialog(Desktop.desktop, "You need to have more than two sequences selected to build a tree!", "Not enough sequences", @@ -2634,9 +2642,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener SequenceGroup sg = viewport.getSelectionGroup(); /* Decide if the selection is a column region */ - while (s < sg.getSize(false)) + while (s < sg.getSize()) { - if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() < + if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg.getEndRes()) { JOptionPane.showMessageDialog(Desktop.desktop, @@ -2779,7 +2787,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener AlignmentView msa = null; if ( (viewport.getSelectionGroup() != null) && - (viewport.getSelectionGroup().getSize(false) > 1)) + (viewport.getSelectionGroup().getSize() > 1)) { // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface! /*SequenceGroup seqs = viewport.getSelectionGroup(); @@ -2821,7 +2829,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener AlignmentView seqs = null; if ( (viewport.getSelectionGroup() != null) && - (viewport.getSelectionGroup().getSize(false) > 0)) + (viewport.getSelectionGroup().getSize() > 0)) { seqs = viewport.getAlignmentView(true); } @@ -2931,28 +2939,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener return tp; } - class PrintThread - extends Thread - { - public void run() - { - PrinterJob printJob = PrinterJob.getPrinterJob(); - PageFormat pf = printJob.pageDialog(printJob.defaultPage()); - printJob.setPrintable(alignPanel, pf); - - if (printJob.printDialog()) - { - try - { - printJob.print(); - } - catch (Exception PrintException) - { - PrintException.printStackTrace(); - } - } - } - } /** * Generates menu items and listener event actions for web service clients @@ -3287,7 +3273,7 @@ public void drop(DropTargetDropEvent evt) } boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport. - alignment, file); + alignment, file, protocol); if (!isAnnotation) { @@ -3355,3 +3341,34 @@ public void drop(DropTargetDropEvent evt) return viewport; } } + +class PrintThread extends Thread +{ + AlignmentPanel ap; + public PrintThread(AlignmentPanel ap) + { + this.ap = ap; + } + static PageFormat pf; + public void run() + { + PrinterJob printJob = PrinterJob.getPrinterJob(); + + if (pf != null) + printJob.setPrintable(ap, pf); + else + printJob.setPrintable(ap); + + if (printJob.printDialog()) + { + try + { + printJob.print(); + } + catch (Exception PrintException) + { + PrintException.printStackTrace(); + } + } + } +}