X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;fp=src%2Fjalview%2Fio%2FFeaturesFile.java;h=df3d352d7bda58a3c14947af472516fcba8fa06d;hb=acc51b96b52db925f7ab71342c6024ef0e8f4b5b;hp=a69788b8bdb1f627822d39ca62ede0cf18b484e1;hpb=2c5026c454594e7299a58b57fe0df3aa563c8d8b;p=jalview.git diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java index a69788b..df3d352 100755 --- a/src/jalview/io/FeaturesFile.java +++ b/src/jalview/io/FeaturesFile.java @@ -21,15 +21,18 @@ package jalview.io; import jalview.analysis.AlignmentUtils; +import jalview.analysis.Finder; import jalview.analysis.SequenceIdMatcher; import jalview.api.AlignViewportI; import jalview.api.FeatureColourI; import jalview.api.FeatureRenderer; import jalview.api.FeaturesSourceI; +import jalview.api.FinderI; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.MappedFeatures; +import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SequenceDummy; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; @@ -85,6 +88,10 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI private static final String ENDFILTERS = "ENDFILTERS"; + private static final String STARTMOTIFS = "STARTMOTIFS"; + + private static final String ENDMOTIFS = "ENDMOTIFS"; + private static final String ID_NOT_SPECIFIED = "ID_NOT_SPECIFIED"; private static final String NOTE = "Note"; @@ -232,6 +239,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI while ((line = nextLine()) != null) { + line = line.trim(); // skip comments/process pragmas if (line.length() == 0 || line.startsWith("#")) { @@ -259,8 +267,9 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI if (gffColumns.length > 0 && gffColumns.length < 4) { /* - * if 2 or 3 tokens, we anticipate either 'startgroup', 'endgroup' or - * a feature type colour specification + * if 2 or 3 tokens, we anticipate one of either + * STARTGROUP ENDGROUP STARTFILTERS STARTMOTIFS + * or a feature type and colour specification */ String ft = gffColumns[0]; if (ft.equalsIgnoreCase(STARTFILTERS)) @@ -268,14 +277,17 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI parseFilters(filters); continue; } + if (ft.equalsIgnoreCase(STARTMOTIFS)) + { + parseMotifs(align, featureGroup); + continue; + } if (ft.equalsIgnoreCase(STARTGROUP)) { featureGroup = gffColumns[1]; } else if (ft.equalsIgnoreCase(ENDGROUP)) { - // We should check whether this is the current group, - // but at present there's no way of showing more than 1 group featureGroup = null; } else @@ -292,8 +304,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI } /* - * if not a comment, GFF pragma, startgroup, endgroup or feature - * colour specification, that just leaves a feature details line + * if not handled above, that just leaves a feature details line * in either Jalview or GFF format */ if (gffVersion == 0) @@ -333,6 +344,62 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI } /** + * Reads lines up to and including the next ENDMOTIFS, and processes each one + * by + *