From 8e2f91c6975f077f4313a516a46a5a42b6388b3a Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Mon, 17 Aug 2015 09:47:12 +0100 Subject: [PATCH] JAL-1831 update all maxItems annotation to the max value for a 32-bit signed binary integer - 2147483674 --- .../json/binding/biojson/v1/AlignmentPojo.java | 27 ++++++++++++++++---- .../binding/biojson/v1/SequenceFeaturesPojo.java | 6 ++++- .../json/binding/biojson/v1/SequenceGrpPojo.java | 7 ++++- .../json/binding/biojson/v1/SequencePojo.java | 6 ++++- 4 files changed, 38 insertions(+), 8 deletions(-) diff --git a/src/jalview/json/binding/biojson/v1/AlignmentPojo.java b/src/jalview/json/binding/biojson/v1/AlignmentPojo.java index 2625b69..dfb60bc 100644 --- a/src/jalview/json/binding/biojson/v1/AlignmentPojo.java +++ b/src/jalview/json/binding/biojson/v1/AlignmentPojo.java @@ -14,16 +14,33 @@ public class AlignmentPojo @Attributes(required = true, description = "Serial version identifier for BioJSON schema") private String svid = "1.0"; - @Attributes(required = true, minItems = 1, maxItems = 1999999999, description = "A sequence group is a bracket of alignment residues spanning
across multiple columns and rows. These can be treated as a
sub-alignments.") + @Attributes( + required = true, + minItems = 1, + maxItems = 2147483647, + description = "A sequence group is a bracket of alignment residues spanning
across multiple columns and rows. These can be treated as a
sub-alignments.") private List seqs = new ArrayList(); - @Attributes(required = false, minItems = 0, maxItems = 1999999999, exclusiveMaximum=true, description = "Alignment annotations stores symbols and graphs usually rendered
below the alignment.") + @Attributes( + required = false, + minItems = 0, + maxItems = 2147483647, + exclusiveMaximum = true, + description = "Alignment annotations stores symbols and graphs usually rendered
below the alignment.") private List alignAnnotation = new ArrayList(); - @Attributes(required = false, minItems = 0, maxItems = 1999999999, description = "A sequence group is a bracket of alignment residues spanning
across multiple columns and rows. These can be treated as a
sub-alignments.") + @Attributes( + required = false, + minItems = 0, + maxItems = 2147483647, + description = "A sequence group is a bracket of alignment residues spanning
across multiple columns and rows. These can be treated as a
sub-alignments.") private List seqGroups = new ArrayList(); - @Attributes(required = false, minItems = 0, maxItems = 1999999999, description = "Sequence features are associated with sequences rather than
alignments. A sequence feature can span across multiple
sequences in an alignment. They indicate features generated
by the same analysis process or retrieved from the same database
(such as Uniprot features).") + @Attributes( + required = false, + minItems = 0, + maxItems = 2147483647, + description = "Sequence features are associated with sequences rather than
alignments. A sequence feature can span across multiple
sequences in an alignment. They indicate features generated
by the same analysis process or retrieved from the same database
(such as Uniprot features).") private List seqFeatures = new ArrayList(); @Attributes(required = false, enums = { "None", "Custom", "Clustal", @@ -96,7 +113,7 @@ public class AlignmentPojo public void setGlobalColorScheme(String globalColorScheme) { -// this.appSettings.put("globalColorScheme", globalColorScheme); + this.appSettings.put("globalColorScheme", globalColorScheme); } public String getColourScheme() diff --git a/src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java b/src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java index e493ecb..4c413c5 100644 --- a/src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java +++ b/src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java @@ -16,7 +16,11 @@ public class SequenceFeaturesPojo @Attributes(required = true, description = "End residue position for the sequence feature") private int xEnd; - @Attributes(required = true, minItems = 1, maxItems = 1999999999, description = "Reference to the sequence in the alignment
(more like a foreign key)") + @Attributes( + required = true, + minItems = 1, + maxItems = 2147483647, + description = "Reference to the sequence in the alignment
(more like a foreign key)") private String sequenceRef; @Attributes(required = true, description = "The name or type of the SequenceFeature") diff --git a/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java b/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java index 63bc426..4bc6e3b 100644 --- a/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java +++ b/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java @@ -36,7 +36,12 @@ public class SequenceGrpPojo @Attributes(required = true, description = "The index of the group’s last residue in the alignment space") private int endRes; - @Attributes(required = true, minItems = 1, maxItems = 1999999999, uniqueItems=true, description = "An array of the unique id's for the sequences belonging to the group") + @Attributes( + required = true, + minItems = 1, + maxItems = 2147483647, + uniqueItems = true, + description = "An array of the unique id's for the sequences belonging to the group") private ArrayList sequenceRefs = new ArrayList(); public String getColourScheme() diff --git a/src/jalview/json/binding/biojson/v1/SequencePojo.java b/src/jalview/json/binding/biojson/v1/SequencePojo.java index 17c6506..5677b13 100644 --- a/src/jalview/json/binding/biojson/v1/SequencePojo.java +++ b/src/jalview/json/binding/biojson/v1/SequencePojo.java @@ -9,7 +9,11 @@ public class SequencePojo @Attributes(required = true, description = "Serial version identifier for the seqs object model") private String svid = "1.0"; - @Attributes(required = true,minLength=3,maxLength=1999999999, description = "Sequence residue characters. An aligned sequence may contain
one of the following gap characters “.”, “-” or “ ”") + @Attributes( + required = true, + minLength = 3, + maxLength = 2147483647, + description = "Sequence residue characters. An aligned sequence may contain
one of the following gap characters “.”, “-” or “ ”") private String seq; @Attributes(required = true, description = "Sequence name") -- 1.7.10.2