From: gmungoc
Date: Wed, 5 Oct 2016 15:17:59 +0000 (+0100)
Subject: Merge branch 'develop' into task/JAL-2196pdbeProperties
X-Git-Tag: Release_2_10_0b1~3^2~17
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e838644df5d5a10a16cf0ad7fb23d24dd7d2729a;hp=6c96743ff6c65895e4b96523d0e3d05f6dc3cb01;p=jalview.git
Merge branch 'develop' into task/JAL-2196pdbeProperties
Conflicts:
src/jalview/datamodel/PDBEntry.java
test/jalview/ws/dbsources/UniprotTest.java
---
diff --git a/RELEASE b/RELEASE
index 6cd9254..c29c5d5 100644
--- a/RELEASE
+++ b/RELEASE
@@ -1,2 +1,2 @@
-jalview.release=Release_2_9_0b1_Branch
-jalview.version=2.9.0b2
+jalview.release=Release_2_10_Branch
+jalview.version=2.10.0
diff --git a/build.xml b/build.xml
index 7feacfb..d8f12e0 100755
--- a/build.xml
+++ b/build.xml
@@ -302,7 +302,7 @@
-
+
@@ -521,7 +521,7 @@
-
+
@@ -573,7 +573,7 @@
-
+
@@ -926,8 +926,7 @@
-
-
+
diff --git a/examples/exampleFeatures.txt b/examples/exampleFeatures.txt
index c0098a9..2de9817 100755
--- a/examples/exampleFeatures.txt
+++ b/examples/exampleFeatures.txt
@@ -79,12 +79,12 @@ Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL
Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL
Fer2 Status: True Positive Pfam 8_8 FER_BRANA -1 8 83 Pfam
Ferredoxin_fold Status: True Positive FER_BRANA -1 2 96 Cath
-Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL
-Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL
-Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL
-Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL
-Fer2 Status: True Positive Pfam 60_13 FER2_ARATH -1 60 135 Pfam
-Ferredoxin_fold Status: True Positive FER2_ARATH -1 50 145 Cath
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 129 129 METAL
+Fer2 Status: True Positive Pfam 60_13 FER1_ARATH -1 60 135 Pfam
+Ferredoxin_fold Status: True Positive FER1_ARATH -1 50 145 Cath
Fer2 Status: True Positive Pfam 60_11 Q93Z60_ARATH -1 60 118 Pfam
Ferredoxin_fold Status: True Positive Q93Z60_ARATH -1 52 118 Cath
Iron-sulfur (2Fe-2S) FER1_MAIZE -1 91 91 METAL
@@ -127,13 +127,13 @@ STARTGROUP netphos
High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 112_11 FER1_SPIOL -1 112 112 PHOSPHORYLATION (S)
High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 139_13 FER1_SPIOL -1 139 139 PHOSPHORYLATION (T)
High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (Y) 73_7 FER1_SPIOL -1 73 73 PHOSPHORYLATION (Y)
-High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 19_1 FER1_ARATH -1 19 19 PHOSPHORYLATION (S)
-High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 24_2 FER1_ARATH -1 24 24 PHOSPHORYLATION (S)
-High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 90_9 FER1_ARATH -1 90 90 PHOSPHORYLATION (S)
-High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 107_10 FER1_ARATH -1 107 107 PHOSPHORYLATION (S)
-High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 114_11 FER1_ARATH -1 114 114 PHOSPHORYLATION (S)
-High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 141_14 FER1_ARATH -1 141 141 PHOSPHORYLATION (T)
-High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (Y) 75_7 FER1_ARATH -1 75 75 PHOSPHORYLATION (Y)
+High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 19_1 FER2_ARATH -1 19 19 PHOSPHORYLATION (S)
+High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 24_2 FER2_ARATH -1 24 24 PHOSPHORYLATION (S)
+High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 90_9 FER2_ARATH -1 90 90 PHOSPHORYLATION (S)
+High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 107_10 FER2_ARATH -1 107 107 PHOSPHORYLATION (S)
+High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 114_11 FER2_ARATH -1 114 114 PHOSPHORYLATION (S)
+High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 141_14 FER2_ARATH -1 141 141 PHOSPHORYLATION (T)
+High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (Y) 75_7 FER2_ARATH -1 75 75 PHOSPHORYLATION (Y)
High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 38_3 FER_BRANA -1 38 38 PHOSPHORYLATION (S)
High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 62_6 FER_BRANA -1 62 62 PHOSPHORYLATION (S)
High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8 FER_BRANA -1 89 89 PHOSPHORYLATION (T)
diff --git a/examples/groovy/featureCounter.groovy b/examples/groovy/featureCounter.groovy
index a16d8bb..9059dd0 100644
--- a/examples/groovy/featureCounter.groovy
+++ b/examples/groovy/featureCounter.groovy
@@ -1,3 +1,24 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
import jalview.workers.FeatureCounterI;
import jalview.workers.AlignmentAnnotationFactory;
diff --git a/examples/plantfdx.fa b/examples/plantfdx.fa
index 1412a5a..f314c85 100644
--- a/examples/plantfdx.fa
+++ b/examples/plantfdx.fa
@@ -35,17 +35,17 @@ IETHKEEELTA-
EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDVT
IETHREEDMV--
>FER1_ARATH/1-148
-----MASTALSSAIVGTSFIRRSPAPISLRSLPSANT-QSLFGLKS-GTARGGRVTAMATYKVKFITPEGEL
-EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVT
-IETHKEEDIV--
+----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
+EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVV
+IETHKEEAIM--
>FER_BRANA/1-96
----------------------------------------------------------ATYKVKFITPEGEQ
EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVT
IETHKEEELV--
>FER2_ARATH/1-148
-----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
-EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVV
-IETHKEEAIM--
+----MASTALSSAIVGTSFIRRSPAPISLRSLPSANT-QSLFGLKS-GTARGGRVTAMATYKVKFITPEGEL
+EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVT
+IETHKEEDIV--
>Q93Z60_ARATH/1-118
----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD--------------------
diff --git a/examples/plantfdx.features b/examples/plantfdx.features
index 872dadc..6a2e058 100644
--- a/examples/plantfdx.features
+++ b/examples/plantfdx.features
@@ -78,23 +78,23 @@ Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL
R -> K FER3_RAPSA -1 91 91 VARIANT
M -> V FER3_RAPSA -1 95 95 VARIANT
Description: Fer2 Status: True Positive Pfam 8_83 FER3_RAPSA -1 8 83 Pfam
-Chloroplast FER1_ARATH -1 1 52 TRANSIT
-Iron-sulfur (2Fe-2S) FER1_ARATH -1 91 91 METAL
-Iron-sulfur (2Fe-2S) FER1_ARATH -1 96 96 METAL
-Iron-sulfur (2Fe-2S) FER1_ARATH -1 99 99 METAL
-Iron-sulfur (2Fe-2S) FER1_ARATH -1 129 129 METAL
-Description: Fer2 Status: True Positive Pfam 60_135 FER1_ARATH -1 60 135 Pfam
-Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL
-Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL
-Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL
-Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL
-Description: Fer2 Status: True Positive Pfam 8_83 FER_BRANA -1 8 83 Pfam
Chloroplast FER2_ARATH -1 1 52 TRANSIT
Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL
Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL
Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL
Description: Fer2 Status: True Positive Pfam 60_135 FER2_ARATH -1 60 135 Pfam
+Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL
+Description: Fer2 Status: True Positive Pfam 8_83 FER_BRANA -1 8 83 Pfam
+Chloroplast FER1_ARATH -1 1 52 TRANSIT
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 129 129 METAL
+Description: Fer2 Status: True Positive Pfam 60_135 FER1_ARATH -1 60 135 Pfam
Description: Fer2 Status: True Positive Pfam 60_118 Q93Z60_ARATH -1 60 118 Pfam
Chloroplast FER1_MAIZE -1 1 52 TRANSIT
STRAND FER1_MAIZE -1 57 59 STRAND
diff --git a/examples/testdata/jal-2005.fa b/examples/testdata/jal-2005.fa
new file mode 100644
index 0000000..cc58469
--- /dev/null
+++ b/examples/testdata/jal-2005.fa
@@ -0,0 +1,16 @@
+>a
+QQQ
+>b
+QQQ
+>c
+QQQ
+>d
+QQQ
+>e
+QQQ
+>f
+QQQ
+>g
+QQQ
+>h
+QQQ
diff --git a/examples/testdata/jal-2005.jvf b/examples/testdata/jal-2005.jvf
new file mode 100644
index 0000000..8f37849
--- /dev/null
+++ b/examples/testdata/jal-2005.jvf
@@ -0,0 +1,11 @@
+feature_1 8c25cd
+
+STARTGROUP Jalview
+feature_1 a -1 1 1 feature_1 0.4
+feature_1 a -1 2 2 feature_1 0.6
+feature_1 b -1 1 1 feature_1 0.8
+feature_1 b -1 2 2 feature_1 1.0
+feature_1 c -1 1 1 feature_1 1.5
+feature_1 d -1 1 1 feature_1 2.0
+feature_1 e -1 1 1 feature_1 3.0
+ENDGROUP Jalview
diff --git a/examples/uniref50.fa b/examples/uniref50.fa
index 72c062d..4bdbfb4 100755
--- a/examples/uniref50.fa
+++ b/examples/uniref50.fa
@@ -35,17 +35,17 @@ TIETHKEEELTA-
QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDV
TIETHREEDMV--
>FER1_ARATH Ferredoxin-1, chloroplast precursor
-MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE
-LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV
-TIETHKEEDIV--
+MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE
+QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV
+VIETHKEEAIM--
>FER_BRANA Ferredoxin
-----------------------------------------------------------ATYKVKFITPEGE
QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV
TIETHKEEELV--
>FER2_ARATH Ferredoxin-2, chloroplast precursor
-MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE
-QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV
-VIETHKEEAIM--
+MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE
+LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV
+TIETHKEEDIV--
>Q93Z60_ARATH At1g10960/T19D16_12
MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE
QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD-------------------
diff --git a/help/help.jhm b/help/help.jhm
index ce98085..7e14204 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -130,6 +130,7 @@
+
@@ -140,10 +141,15 @@
+
+
+
+
+
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index a6145c1..bf1710c 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -23,11 +23,9 @@
-
-
-
-
-
+
+
+
@@ -158,9 +156,11 @@
+
+
+
-
diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html
index c870887..2ade2e0 100644
--- a/help/html/calculations/consensus.html
+++ b/help/html/calculations/consensus.html
@@ -43,7 +43,7 @@
entry from the consensus annotation label to copy the alignment's
consensus sequence to the clipboard.
- Sequence logo
+ Sequence logo
By clicking on the label you can also activate the sequence logo. It
indicates the relative amount of residues per column which can be
diff --git a/help/html/calculations/referenceseq.html b/help/html/calculations/referenceseq.html
index 03d24a5..912be55 100644
--- a/help/html/calculations/referenceseq.html
+++ b/help/html/calculations/referenceseq.html
@@ -26,25 +26,47 @@
Reference Sequence Alignment Views
+ Many alignment analysis tasks concern a query, or reference
+ sequence. For instance, when searching for sequences from other
+ organisms that are similar to a newly sequenced gene, or when
+ searching for structurally similar sequences for use in homology
+ modelling.
+
+ What happens when a reference sequence is defined ?
+
The reference sequence for an alignment is indicated by its ID being
- shown in bold. When a reference sequence has been defined, the Format→Show
- unconserved option highlights mutations with respect to the
- reference sequence, rather than the alignment's consensus sequence.
-
+ shown in bold. In addition:
+
+ - Reference sequence numbering. Instead of
+ column numbers, the alignment ruler shows the reference sequence
+ positions at each column. At each tick mark, either the reference
+ sequence symbol and position is given, or the column number when a
+ gap is present at that position in the reference sequence.
+ - Format→Show unconserved highlights
+ mutations with respect to the reference sequence, rather than the
+ alignment's consensus sequence.
+
+ Defining the reference sequence
+
+ Each alignment view can have its own reference sequence.
- - Jalview automatically assigns a reference sequence when JPred4 predictions are imported.
-
- - Assigning a reference sequence
A
- sequence can be marked as the reference sequence by right-clicking
- on it's ID to open the popup menu, and selecting the "(Sequence
- ID)→Mark as Reference" entry."
+ - Manually assigning a reference sequence
+ A sequence can be marked as the reference sequence by
+ right-clicking on its ID to open the popup menu, and selecting the
+ "(Sequence ID)→Mark as Reference" entry.
+ - Defining a reference when importing
+ annotation
Jalview automatically assigns a reference
+ sequence when importing analysis results, such as those returned
+ from JPred4 . A reference
+ sequence can also be assigned via the SET_REF command in
+ an alignment annotation file.
Reference sequence based alignment visualisation was
- introduced in Jalview 2.9.
+ introduced in Jalview 2.9, and support for storage and retrieval
+ of reference sequence views in 2.10.