X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=cd9c5337c23744694350cacc5292b7ca24791f4e;hb=2a9991ef1eb02d97e9c8ed1644f292117ae6f600;hp=b13a3904d6f206fc48dd05c9783fcd031b2795cb;hpb=fe9a5fd35b336b3ddd45e016d66bf5203f47c047;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index b13a390..cd9c533 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -20,6 +20,52 @@ */ package jalview.gui; +import java.awt.BorderLayout; +import java.awt.Component; +import java.awt.Rectangle; +import java.awt.Toolkit; +import java.awt.datatransfer.Clipboard; +import java.awt.datatransfer.DataFlavor; +import java.awt.datatransfer.StringSelection; +import java.awt.datatransfer.Transferable; +import java.awt.dnd.DnDConstants; +import java.awt.dnd.DropTargetDragEvent; +import java.awt.dnd.DropTargetDropEvent; +import java.awt.dnd.DropTargetEvent; +import java.awt.dnd.DropTargetListener; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.KeyAdapter; +import java.awt.event.KeyEvent; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.awt.print.PageFormat; +import java.awt.print.PrinterJob; +import java.beans.PropertyChangeEvent; +import java.io.File; +import java.net.URL; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Deque; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.Set; +import java.util.Vector; + +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JEditorPane; +import javax.swing.JInternalFrame; +import javax.swing.JLayeredPane; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.JScrollPane; +import javax.swing.SwingUtilities; + import jalview.analysis.AAFrequency; import jalview.analysis.AlignmentSorter; import jalview.analysis.AlignmentUtils; @@ -52,6 +98,7 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; import jalview.datamodel.AlignmentView; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenSequences; import jalview.datamodel.PDBEntry; import jalview.datamodel.SeqCigar; import jalview.datamodel.Sequence; @@ -97,52 +144,6 @@ import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.seqfetcher.DbSourceProxy; -import java.awt.BorderLayout; -import java.awt.Component; -import java.awt.Rectangle; -import java.awt.Toolkit; -import java.awt.datatransfer.Clipboard; -import java.awt.datatransfer.DataFlavor; -import java.awt.datatransfer.StringSelection; -import java.awt.datatransfer.Transferable; -import java.awt.dnd.DnDConstants; -import java.awt.dnd.DropTargetDragEvent; -import java.awt.dnd.DropTargetDropEvent; -import java.awt.dnd.DropTargetEvent; -import java.awt.dnd.DropTargetListener; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.ItemEvent; -import java.awt.event.ItemListener; -import java.awt.event.KeyAdapter; -import java.awt.event.KeyEvent; -import java.awt.event.MouseAdapter; -import java.awt.event.MouseEvent; -import java.awt.print.PageFormat; -import java.awt.print.PrinterJob; -import java.beans.PropertyChangeEvent; -import java.io.File; -import java.net.URL; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Deque; -import java.util.Enumeration; -import java.util.Hashtable; -import java.util.List; -import java.util.Set; -import java.util.Vector; - -import javax.swing.JCheckBoxMenuItem; -import javax.swing.JEditorPane; -import javax.swing.JInternalFrame; -import javax.swing.JLayeredPane; -import javax.swing.JMenu; -import javax.swing.JMenuItem; -import javax.swing.JOptionPane; -import javax.swing.JRadioButtonMenuItem; -import javax.swing.JScrollPane; -import javax.swing.SwingUtilities; - /** * DOCUMENT ME! * @@ -239,6 +240,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, this(al, hiddenColumns, width, height, null); } + /** * Create alignment frame for al with hiddenColumns, a specific width and * height, and specific sequenceId @@ -288,6 +290,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, init(); } + public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, + ColumnSelection hiddenColumns, int width, int height) + { + setSize(width, height); + + if (al.getDataset() == null) + { + al.setDataset(null); + } + + viewport = new AlignViewport(al, hiddenColumns); + + if (hiddenSeqs != null && hiddenSeqs.length > 0) + { + viewport.hideSequence(hiddenSeqs); + viewport.setHasHiddenRows(true); + } + alignPanel = new AlignmentPanel(this, viewport); + addAlignmentPanel(alignPanel, true); + init(); + } + + /** * Make a new AlignFrame from existing alignmentPanels * @@ -1097,11 +1122,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .lastIndexOf(java.io.File.separatorChar) + 1); } - /* - * First save any linked Chimera session. - */ - Desktop.instance.saveChimeraSessions(file); - success = new Jalview2XML().saveAlignment(this, file, shortName); statusBar.setText(MessageManager.formatMessage( @@ -1120,32 +1140,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return false; } - String[] omitHidden = null; - - if (viewport.hasHiddenColumns()) - { - int reply = JOptionPane - .showInternalConfirmDialog( - Desktop.desktop, - MessageManager - .getString("label.alignment_contains_hidden_columns"), - MessageManager - .getString("action.save_omit_hidden_columns"), - JOptionPane.YES_NO_OPTION, - JOptionPane.QUESTION_MESSAGE); - - if (reply == JOptionPane.YES_OPTION) - { - omitHidden = viewport.getViewAsString(false); - } - } - FeatureRenderer fr = new FeatureRenderer(this.alignPanel); - viewport.setFeatureRenderer(fr); + ExportData exportData = getAlignmentForExport(); FormatAdapter f = new FormatAdapter(viewport); String output = f.formatSequences(format, - viewport.getAlignment(), // class cast exceptions will + exportData.getAlignment(), // class cast exceptions will // occur in the distant future - omitHidden, f.getCacheSuffixDefault(format), + exportData.getOmitHidden(), exportData.getStartEndPostions(), + f.getCacheSuffixDefault(format), viewport.getColumnSelection()); if (output == null) @@ -1186,6 +1187,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return success; } + private void warningMessage(String warning, String title) { if (new jalview.util.Platform().isHeadless()) @@ -1210,10 +1212,45 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void outputText_actionPerformed(ActionEvent e) { + + ExportData exportData = getAlignmentForExport(); + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + cap.setForInput(null); + + try + { + cap.setText(new FormatAdapter(viewport).formatSequences( + e.getActionCommand(), + exportData.getAlignment(), + exportData.getOmitHidden(), exportData.getStartEndPostions(), + viewport.getColumnSelection())); + Desktop.addInternalFrame(cap, MessageManager.formatMessage( + "label.alignment_output_command", new Object[] + { e.getActionCommand() }), 600, 500); + } catch (OutOfMemoryError oom) + { + new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom); + cap.dispose(); + } + + } + + public ExportData getAlignmentForExport() + { + AlignmentI alignmentToExport = null; String[] omitHidden = null; + int[] alignmentStartEnd = new int[2]; FeatureRenderer fr = new FeatureRenderer(this.alignPanel); viewport.setFeatureRenderer(fr); - if (viewport.hasHiddenColumns()) + HiddenSequences hiddenSeqs = viewport.getAlignment() + .getHiddenSequences(); + + + alignmentToExport = viewport.getAlignment(); + alignmentStartEnd = new int[] + { 0, alignmentToExport.getWidth() - 1 }; + + if (viewport.hasHiddenColumns() || hiddenSeqs.getSize() > 0) { int reply = JOptionPane .showInternalConfirmDialog( @@ -1227,28 +1264,83 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (reply == JOptionPane.YES_OPTION) { + // export only visible region omitHidden = viewport.getViewAsString(false); + alignmentToExport = viewport.getAlignment(); + alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport + .getColumnSelection().getHiddenColumns()); + viewport.setIncludeHiddenRegion(false); + } + else + { + // export all region including visible + alignmentToExport = hiddenSeqs.getFullAlignment(); + viewport.setIncludeHiddenRegion(true); } } - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - cap.setForInput(null); + return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd); + } - try + private static int[] getStartEnd(int[] aligmentStartEnd, + List hiddenCols) + { + int startPos = aligmentStartEnd[0]; + int endPos = aligmentStartEnd[1]; + + int[] lowestRange = new int[2]; + int[] higestRange = new int[2]; + + for (int[] hiddenCol : hiddenCols) { - cap.setText(new FormatAdapter(viewport).formatSequences( - e.getActionCommand(), - viewport.getAlignment(), omitHidden, - viewport.getColumnSelection())); - Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.alignment_output_command", new Object[] - { e.getActionCommand() }), 600, 500); - } catch (OutOfMemoryError oom) + // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]); + + lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange; + higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange; + } + // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]); + // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]); + + if (lowestRange[0] == 0 && lowestRange[1] == 0) { - new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom); - cap.dispose(); + startPos = aligmentStartEnd[0]; + } + else + { + startPos = lowestRange[1] + 1; } + if (higestRange[0] == 0 && higestRange[1] == 0) + { + endPos = aligmentStartEnd[1]; + } + else + { + endPos = higestRange[0]; + } + + // System.out.println("Export range : " + minPos + " - " + maxPos); + return new int[] + { startPos, endPos }; + } + + public static void main(String[] args) + { + ArrayList hiddenCols = new ArrayList(); + hiddenCols.add(new int[] + { 0, 4 }); + hiddenCols.add(new int[] + { 6, 9 }); + hiddenCols.add(new int[] + { 11, 12 }); + hiddenCols.add(new int[] + { 33, 33 }); + hiddenCols.add(new int[] + { 45, 50 }); + + int[] x = getStartEnd(new int[] + { 0, 50 }, hiddenCols); + // System.out.println("Export range : " + x[0] + " - " + x[1]); } /** @@ -1775,7 +1867,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } String output = new FormatAdapter().formatSequences("Fasta", seqs, - omitHidden); + omitHidden, null); StringSelection ss = new StringSelection(output); @@ -5987,6 +6079,53 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sf.setComplementVisible(this, show); } } + + public class ExportData + { + private AlignmentI alignment; + + private String[] omitHidden; + + private int[] startEnd; + + public ExportData(AlignmentI align, String[] ommit, int[] startEnd) + { + this.alignment = align; + this.omitHidden = ommit; + this.startEnd = startEnd; + } + + public AlignmentI getAlignment() + { + return alignment; + } + + public void setAlignment(AlignmentI alignment) + { + this.alignment = alignment; + } + + public String[] getOmitHidden() + { + return omitHidden; + } + + public void setOmitHidden(String[] omitHidden) + { + this.omitHidden = omitHidden; + } + + public int[] getStartEndPostions() + { + return startEnd; + } + + public void setStartEndPostions(int[] startEnd) + { + this.startEnd = startEnd; + } + } + } class PrintThread extends Thread