From: gmungoc
Date: Thu, 26 May 2016 13:05:02 +0000 (+0100)
Subject: Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
X-Git-Tag: Release_2_10_0~212^2~4^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b2812af7b64b3ee81d0c5a50ff9a2cd0bcbd0de1;hp=e879efcd79694e43a8081c9235a13740cb429076;p=jalview.git
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
---
diff --git a/examples/exampleFeatures.txt b/examples/exampleFeatures.txt
index 2dc4b6d..63c8326 100755
--- a/examples/exampleFeatures.txt
+++ b/examples/exampleFeatures.txt
@@ -30,69 +30,69 @@ Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL
-Fer2 Status: True Positive Pfam 8_8 FER_CAPAA -1 8 83 Pfam
+Fer2 Status: True Positive Pfam 8_8 FER_CAPAA -1 8 83 Pfam
Ferredoxin_fold Status: True Positive FER_CAPAA -1 3 93 Cath
Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL
-Fer2 Status: True Positive Pfam 55_13 FER_CAPAN -1 55 130 Pfam
+Fer2 Status: True Positive Pfam 55_13 FER_CAPAN -1 55 130 Pfam
Ferredoxin_fold Status: True Positive FER_CAPAN -1 45 140 Cath
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL
-Fer2 Status: True Positive Pfam 55_13 FER1_SOLLC -1 55 130 Pfam
+Fer2 Status: True Positive Pfam 55_13 FER1_SOLLC -1 55 130 Pfam
Ferredoxin_fold Status: True Positive FER1_SOLLC -1 45 140 Cath
-Fer2 Status: True Positive Pfam 55_13 Q93XJ9_SOLTU -1 55 130 Pfam
+Fer2 Status: True Positive Pfam 55_13 Q93XJ9_SOLTU -1 55 130 Pfam
Ferredoxin_fold Status: True Positive Q93XJ9_SOLTU -1 45 140 Cath
Iron-sulfur (2Fe-2S) FER1_PEA -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL
Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL
Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL
-Fer2 Status: True Positive Pfam 60_13 FER1_PEA -1 60 135 Pfam
+Fer2 Status: True Positive Pfam 60_13 FER1_PEA -1 60 135 Pfam
Ferredoxin_fold Status: True Positive FER1_PEA -1 50 145 Cath
-Fer2 Status: True Positive Pfam 63_13 Q7XA98_TRIPR -1 63 138 Pfam
+Fer2 Status: True Positive Pfam 63_13 Q7XA98_TRIPR -1 63 138 Pfam
Ferredoxin_fold Status: True Positive Q7XA98_TRIPR -1 53 148 Cath
Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL
-Fer2 Status: True Positive Pfam 59_13 FER1_MESCR -1 59 134 Pfam
+Fer2 Status: True Positive Pfam 59_13 FER1_MESCR -1 59 134 Pfam
Ferredoxin_fold Status: True Positive FER1_MESCR -1 49 144 Cath
Iron-sulfur (2Fe-2S) FER1_SPIOL -1 89 89 METAL
Iron-sulfur (2Fe-2S) FER1_SPIOL -1 94 94 METAL
Iron-sulfur (2Fe-2S) FER1_SPIOL -1 97 97 METAL
Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL
-Fer2 Status: True Positive Pfam 58_13 FER1_SPIOL -1 58 133 Pfam
+Fer2 Status: True Positive Pfam 58_13 FER1_SPIOL -1 58 133 Pfam
Ferredoxin_fold Status: True Positive FER1_SPIOL -1 48 143 Cath
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 47 47 METAL
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL
-Fer2 Status: True Positive Pfam 8_8 FER3_RAPSA -1 8 83 Pfam
+Fer2 Status: True Positive Pfam 8_8 FER3_RAPSA -1 8 83 Pfam
Ferredoxin_fold Status: True Positive FER3_RAPSA -1 3 93 Cath
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
-Fer2 Status: True Positive Pfam 8_8 FER_BRANA -1 8 83 Pfam
+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
+Fer2 Status: True Positive Pfam 60_13 FER2_ARATH -1 60 135 Pfam
Ferredoxin_fold Status: True Positive FER2_ARATH -1 50 145 Cath
-Fer2 Status: True Positive Pfam 60_11 Q93Z60_ARATH -1 60 118 Pfam
+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
Iron-sulfur (2Fe-2S) FER1_MAIZE -1 96 96 METAL
Iron-sulfur (2Fe-2S) FER1_MAIZE -1 99 99 METAL
Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL
-Fer2 Status: True Positive Pfam 60_13 FER1_MAIZE -1 60 135 Pfam
+Fer2 Status: True Positive Pfam 60_13 FER1_MAIZE -1 60 135 Pfam
Ferredoxin_fold Status: True Positive FER1_MAIZE -1 50 145 Cath
-Fer2 Status: True Positive Pfam 52_12 O80429_MAIZE -1 52 127 Pfam
+Fer2 Status: True Positive Pfam 52_12 O80429_MAIZE -1 52 127 Pfam
Ferredoxin_fold Status: True Positive O80429_MAIZE -1 42 137 Cath
ENDGROUP uniprot
diff --git a/examples/plantfdx.features b/examples/plantfdx.features
index a23d152..872dadc 100644
--- a/examples/plantfdx.features
+++ b/examples/plantfdx.features
@@ -14,22 +14,22 @@ Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL
-Description: Fer2 Status: True Positive Pfam 8_83 FER_CAPAA -1 8 83 Pfam
+Description: Fer2 Status: True Positive Pfam 8_83 FER_CAPAA -1 8 83 Pfam
Chloroplast FER_CAPAN -1 1 47 TRANSIT
Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL
Phosphothreonine FER_CAPAN -1 136 136 MOD_RES
-Description: Fer2 Status: True Positive Pfam 55_130 FER_CAPAN -1 55 130 Pfam
+Description: Fer2 Status: True Positive Pfam 55_130 FER_CAPAN -1 55 130 Pfam
Chloroplast FER1_SOLLC -1 1 47 TRANSIT
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL
-Description: Fer2 Status: True Positive Pfam 55_130 FER1_SOLLC -1 55 130 Pfam
+Description: Fer2 Status: True Positive Pfam 55_130 FER1_SOLLC -1 55 130 Pfam
Evidence: EI4 Q93XJ9_SOLTU -1 1 48 SIGNAL
-Description: Fer2 Status: True Positive Pfam 55_130 Q93XJ9_SOLTU -1 55 130 Pfam
+Description: Fer2 Status: True Positive Pfam 55_130 Q93XJ9_SOLTU -1 55 130 Pfam
Chloroplast FER1_PEA -1 1 52 TRANSIT
L -> I (in strain: cv. Onward) FER1_PEA -1 59 59 VARIANT
I -> L (in strain: cv. Onward) FER1_PEA -1 85 85 VARIANT
@@ -38,14 +38,14 @@ Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL
Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL
Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL
YPTS -> PPPA (in Ref. 2) FER1_PEA -1 132 135 CONFLICT
-Description: Fer2 Status: True Positive Pfam 60_135 FER1_PEA -1 60 135 Pfam
-Description: Fer2 Status: True Positive Pfam 63_138 Q7XA98_TRIPR -1 63 138 Pfam
+Description: Fer2 Status: True Positive Pfam 60_135 FER1_PEA -1 60 135 Pfam
+Description: Fer2 Status: True Positive Pfam 63_138 Q7XA98_TRIPR -1 63 138 Pfam
Chloroplast FER1_MESCR -1 1 51 TRANSIT
Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL
-Description: Fer2 Status: True Positive Pfam 59_134 FER1_MESCR -1 59 134 Pfam
+Description: Fer2 Status: True Positive Pfam 59_134 FER1_MESCR -1 59 134 Pfam
Chloroplast FER1_SPIOL -1 1 50 TRANSIT
STRAND FER1_SPIOL -1 52 59 STRAND
TURN FER1_SPIOL -1 60 61 TURN
@@ -68,7 +68,7 @@ Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL
STRAND FER1_SPIOL -1 130 133 STRAND
STRAND FER1_SPIOL -1 135 138 STRAND
HELIX FER1_SPIOL -1 142 144 HELIX
-Description: Fer2 Status: True Positive Pfam 58_133 FER1_SPIOL -1 58 133 Pfam
+Description: Fer2 Status: True Positive Pfam 58_133 FER1_SPIOL -1 58 133 Pfam
I -> V FER3_RAPSA -1 8 8 VARIANT
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL
@@ -77,25 +77,25 @@ S -> T FER3_RAPSA -1 55 55 VARIANT
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
+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
+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
+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
-Description: Fer2 Status: True Positive Pfam 60_118 Q93Z60_ARATH -1 60 118 Pfam
+Description: Fer2 Status: True Positive Pfam 60_135 FER2_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
STRAND FER1_MAIZE -1 72 74 STRAND
@@ -113,6 +113,6 @@ Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL
STRAND FER1_MAIZE -1 132 135 STRAND
STRAND FER1_MAIZE -1 137 141 STRAND
TURN FER1_MAIZE -1 142 142 TURN
-Description: Fer2 Status: True Positive Pfam 60_135 FER1_MAIZE -1 60 135 Pfam
-Description: Fer2 Status: True Positive Pfam 52_127 O80429_MAIZE -1 52 127 Pfam
+Description: Fer2 Status: True Positive Pfam 60_135 FER1_MAIZE -1 60 135 Pfam
+Description: Fer2 Status: True Positive Pfam 52_127 O80429_MAIZE -1 52 127 Pfam
ENDGROUP uniprot
diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html
index 9164afd..200fc8f 100755
--- a/help/html/features/featuresettings.html
+++ b/help/html/features/featuresettings.html
@@ -104,7 +104,7 @@
the bottom of the list is rendered below a feature higher
up in the list.
You can change
the order of a feature by dragging it up and down the list with
- the mouse.
+ the mouse (not applet).
The Optimise order button (currently only
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index d4ae57d..7b3ce25 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -235,10 +235,7 @@ public class Conservation
c = '-';
}
- if (!canonicaliseAa && 'a' <= c && c <= 'z')
- {
- c -= (32); // 32 = 'a' - 'A'
- }
+ c = toUpperCase(c);
}
values[c]++;
}
@@ -326,6 +323,7 @@ public class Conservation
}
else
{
+ c = toUpperCase(c);
nres++;
if (nres == 1)
@@ -347,6 +345,22 @@ public class Conservation
}
/**
+ * Returns the upper-cased character if between 'a' and 'z', else the
+ * unchanged value
+ *
+ * @param c
+ * @return
+ */
+ char toUpperCase(char c)
+ {
+ if ('a' <= c && c <= 'z')
+ {
+ c -= (32); // 32 = 'a' - 'A'
+ }
+ return c;
+ }
+
+ /**
* Calculates the conservation sequence
*
* @param consflag
diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index 81d5b05..73d8826 100644
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -104,7 +104,7 @@ public class FeaturesFileTest
sf = sfs[4];
assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
sf.description);
- assertEquals("Pfam 8_8|http://pfam.sanger.ac.uk/family/PF00111",
+ assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
sf.links.get(0).toString());
assertEquals(8, sf.begin);
assertEquals(83, sf.end);
@@ -428,7 +428,7 @@ public class FeaturesFileTest
+ "STARTGROUP\tuniprot\n"
+ "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
+ "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
- + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\n"
+ + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\n"
+ "ENDGROUP\tuniprot\n";
FeaturesFile featuresFile = new FeaturesFile(features,
FormatAdapter.PASTE);
@@ -478,7 +478,7 @@ public class FeaturesFileTest
+ "\nSTARTGROUP\tuniprot\n"
+ "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
+ "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
- + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n"
+ + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n"
+ "ENDGROUP\tuniprot\n";
assertEquals(expected, exported);
}