/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.io;
-import jalview.api.AlignViewportI;
-import jalview.datamodel.*;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
/**
* Additional formatting methods used by the application in a number of places.
*/
public class FormatAdapter extends AppletFormatAdapter
{
+ public FormatAdapter(AlignmentViewPanel viewpanel)
+ {
+ super(viewpanel);
+ init();
+ }
+
+ public FormatAdapter()
+ {
+ super();
+ init();
+ }
+
+ public FormatAdapter(AlignmentViewPanel alignPanel,
+ AlignExportSettingI settings)
+ {
+ super(alignPanel, settings);
+ }
+
+ private void init()
+ {
+ if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
+ {
+ annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
+ true);
+ localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
+ true);
+ serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+ true);
+ }
+ else
+ {
+ // disable all PDB annotation options
+ annotFromStructure = false;
+ localSecondaryStruct = false;
+ serviceSecondaryStruct = false;
+ }
+ }
public String formatSequences(String format, SequenceI[] seqs,
- String[] omitHiddenColumns)
+ String[] omitHiddenColumns, int[] exportRange)
{
- return formatSequences(format, replaceStrings(seqs, omitHiddenColumns));
+ return formatSequences(format,
+ replaceStrings(seqs, omitHiddenColumns, exportRange));
}
/**
* @return new sequences
*/
public SequenceI[] replaceStrings(SequenceI[] seqs,
- String[] omitHiddenColumns)
+ String[] omitHiddenColumns, int[] startEnd)
{
if (omitHiddenColumns != null)
{
SequenceI[] tmp = new SequenceI[seqs.length];
+
+ int startRes;
+ int endRes;
+ int startIndex;
+ int endIndex;
for (int i = 0; i < seqs.length; i++)
{
+ startRes = seqs[i].getStart();
+ endRes = seqs[i].getEnd();
+
+ if (startEnd != null)
+ {
+ startIndex = startEnd[0];
+ endIndex = startEnd[1];
+ // get first non-gaped residue start position
+ while (jalview.util.Comparison.isGap(seqs[i]
+ .getCharAt(startIndex)) && startIndex < endIndex)
+ {
+ startIndex++;
+ }
+
+ // get last non-gaped residue end position
+ while (jalview.util.Comparison.isGap(seqs[i].getCharAt(endIndex))
+ && endIndex > startIndex)
+ {
+ endIndex--;
+ }
+
+ startRes = seqs[i].findPosition(startIndex);
+ startRes = seqs[i].getStart() > 1 ? startRes - seqs[i].getStart()
+ : startRes;
+ endRes = seqs[i].findPosition(endIndex) - seqs[i].getStart();
+ }
+
tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],
- seqs[i].getStart(), seqs[i].getEnd());
+ startRes, endRes);
tmp[i].setDescription(seqs[i].getDescription());
}
seqs = tmp;
public boolean getCacheSuffixDefault(String format)
{
if (isValidFormat(format))
+ {
return jalview.bin.Cache.getDefault(format.toUpperCase()
+ "_JVSUFFIX", true);
+ }
return false;
}
public String formatSequences(String format, AlignmentI alignment,
- String[] omitHidden, ColumnSelection colSel)
+ String[] omitHidden, int[] exportRange, ColumnSelection colSel)
{
- return formatSequences(format, alignment, omitHidden,
+ return formatSequences(format, alignment, omitHidden, exportRange,
getCacheSuffixDefault(format), colSel, null);
}
public String formatSequences(String format, AlignmentI alignment,
- String[] omitHidden, ColumnSelection colSel, SequenceGroup sgp)
+ String[] omitHidden, int[] exportRange, ColumnSelection colSel,
+ SequenceGroup sgp)
{
- return formatSequences(format, alignment, omitHidden,
+ return formatSequences(format, alignment, omitHidden, exportRange,
getCacheSuffixDefault(format), colSel, sgp);
}
* @return string representation of the alignment formatted as format
*/
public String formatSequences(String format, AlignmentI alignment,
- String[] omitHidden, boolean suffix, ColumnSelection colSel)
+ String[] omitHidden, int[] exportRange, boolean suffix,
+ ColumnSelection colSel)
{
- return formatSequences(format, alignment, omitHidden, suffix, colSel,
- null);
+ return formatSequences(format, alignment, omitHidden, exportRange,
+ suffix, colSel, null);
}
public String formatSequences(String format, AlignmentI alignment,
- String[] omitHidden, boolean suffix, ColumnSelection colSel,
- jalview.datamodel.SequenceGroup selgp)
+ String[] omitHidden, int[] exportRange, boolean suffix,
+ ColumnSelection colSel, jalview.datamodel.SequenceGroup selgp)
{
if (omitHidden != null)
{
// TODO: JAL-1486 - set start and end for output correctly. basically,
// AlignmentView.getVisibleContigs does this.
Alignment alv = new Alignment(replaceStrings(
- alignment.getSequencesArray(), omitHidden));
+ alignment.getSequencesArray(), omitHidden, exportRange));
AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
if (ala != null)
{
return this.formatSequences(format, alignment, suffix);
}
+ public AlignmentI readFile(String inFile, String type, String format)
+ throws java.io.IOException
+ {
+ AlignmentI al = super.readFile(inFile, type, format);
+ return al;
+ }
+
+ public AlignmentI readFromFile(FileParse source, String format)
+ throws java.io.IOException
+ {
+ AlignmentI al = super.readFromFile(source, format);
+ return al;
+ }
+
/**
* validate format is valid for IO in Application. This is basically the
* AppletFormatAdapter.isValidFormat call with additional checks for
}
/**
- * Create a flat file representation of a given view or selected region of a view
+ * Create a flat file representation of a given view or selected region of a
+ * view
+ *
* @param format
- * @param av
+ * @param ap
+ * alignment panel originating the view
* @return String containing flat file
*/
- public String formatSequences(String format, AlignViewportI av, boolean selectedOnly)
+ public String formatSequences(String format, AlignmentViewPanel ap,
+ boolean selectedOnly)
{
- return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
+ return formatSequences(format, getCacheSuffixDefault(format), ap,
+ selectedOnly);
}
}
git://source.jalview.org / jalview.git / blobdiff