X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=eac1041b9d8625cc4fc3f6e3b3263961396637ca;hb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;hp=dfbdf86f14dc01f4460b06cb3ce7d6cfcc38b04b;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java index dfbdf86..eac1041 100755 --- a/src/jalview/io/FormatAdapter.java +++ b/src/jalview/io/FormatAdapter.java @@ -20,7 +20,9 @@ */ package jalview.io; -import jalview.api.AlignViewportI; +import jalview.api.AlignExportSettingI; +import jalview.api.AlignmentViewPanel; +import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; @@ -29,6 +31,8 @@ import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import java.io.IOException; + /** * Additional formatting methods used by the application in a number of places. * @@ -37,18 +41,34 @@ import jalview.datamodel.SequenceI; */ 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); + true); + serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW", + true); } else { @@ -58,11 +78,13 @@ public class FormatAdapter extends AppletFormatAdapter 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)); } /** @@ -74,15 +96,44 @@ public class FormatAdapter extends AppletFormatAdapter * @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); + endRes = seqs[i].findPosition(endIndex); + } + 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; @@ -177,27 +228,28 @@ public class FormatAdapter extends AppletFormatAdapter return null; } - public boolean getCacheSuffixDefault(String format) + public boolean getCacheSuffixDefault(FileFormatI format) { if (isValidFormat(format)) { - return jalview.bin.Cache.getDefault(format.toUpperCase() + return Cache.getDefault(format.toUpperCase() + "_JVSUFFIX", true); } return false; } - public String formatSequences(String format, AlignmentI alignment, - String[] omitHidden, ColumnSelection colSel) + public String formatSequences(FileFormatI format, AlignmentI alignment, + 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) + public String formatSequences(FileFormatI format, AlignmentI alignment, + String[] omitHidden, int[] exportRange, ColumnSelection colSel, + SequenceGroup sgp) { - return formatSequences(format, alignment, omitHidden, + return formatSequences(format, alignment, omitHidden, exportRange, getCacheSuffixDefault(format), colSel, sgp); } @@ -213,16 +265,17 @@ public class FormatAdapter extends AppletFormatAdapter * defines hidden columns that are edited out of annotation * @return string representation of the alignment formatted as format */ - public String formatSequences(String format, AlignmentI alignment, - String[] omitHidden, boolean suffix, ColumnSelection colSel) + public String formatSequences(FileFormatI format, AlignmentI alignment, + 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) + public String formatSequences(FileFormatI format, AlignmentI alignment, + String[] omitHidden, int[] exportRange, boolean suffix, + ColumnSelection colSel, SequenceGroup selgp) { if (omitHidden != null) { @@ -231,7 +284,7 @@ public class FormatAdapter extends AppletFormatAdapter // 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) { @@ -255,38 +308,19 @@ public class FormatAdapter extends AppletFormatAdapter return this.formatSequences(format, alignment, suffix); } - public Alignment readFile(String inFile, String type, String format) - throws java.io.IOException + @Override + public AlignmentI readFile(String file, DataSourceType sourceType, + FileFormatI fileFormat) throws IOException { - Alignment al; - if (format.equals("HTML")) - { - afile = new HtmlFile(inFile, type); - al = new Alignment(afile.getSeqsAsArray()); - afile.addAnnotations(al); - } - else - { - al = super.readFile(inFile, type, format); - } - + AlignmentI al = super.readFile(file, sourceType, fileFormat); return al; } - public AlignmentI readFromFile(FileParse source, String format) - throws java.io.IOException + @Override + public AlignmentI readFromFile(FileParse source, FileFormatI format) + throws IOException { - Alignment al; - if (format.equals("HTML")) - { - afile = new HtmlFile(source); - al = new Alignment(afile.getSeqsAsArray()); - afile.addAnnotations(al); - } - else - { - al = (Alignment) super.readFromFile(source, format); - } + AlignmentI al = super.readFromFile(source, format); return al; } @@ -313,14 +347,19 @@ public class FormatAdapter extends AppletFormatAdapter } /** - * 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(FileFormatI format, AlignmentViewPanel ap, + boolean selectedOnly) { - return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly); + return formatSequences(format, getCacheSuffixDefault(format), ap, + selectedOnly); } }