*/
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;
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;
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!
*
this(al, hiddenColumns, width, height, null);
}
+
/**
* Create alignment frame for al with hiddenColumns, a specific width and
* height, and specific sequenceId
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
*
.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(
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)
return success;
}
+
private void warningMessage(String warning, String title)
{
if (new jalview.util.Platform().isHeadless())
@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(
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<int[]> 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<int[]> hiddenCols = new ArrayList<int[]>();
+ 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]);
}
/**
}
String output = new FormatAdapter().formatSequences("Fasta", seqs,
- omitHidden);
+ omitHidden, null);
StringSelection ss = new StringSelection(output);
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
git://source.jalview.org / jalview.git / blobdiff