From: Jim Procter Date: Thu, 26 May 2016 14:21:24 +0000 (+0100) Subject: Merge branch 'develop' of http://source.jalview.org/git/jalview into develop X-Git-Tag: Release_2_10_0~212^2~4 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e00d0cbf84f4a2a21a927e9c017c3a69fc436704;hp=a66ef4094d32ee13d64bb63139fe3cb33c3a04dc;p=jalview.git Merge branch 'develop' of source.jalview.org/git/jalview into develop --- diff --git a/examples/exampleFeatures.txt b/examples/exampleFeatures.txt index 2dc4b6d..c0098a9 100755 --- a/examples/exampleFeatures.txt +++ b/examples/exampleFeatures.txt @@ -26,73 +26,74 @@ BETA-TURN-IIL 8b5b50 ST-MOTIF ac25a1 STARTGROUP uniprot +Pfam family FER_CAPAA -1 0 0 Pfam 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/help/html/features/mmcif.html b/help/html/features/mmcif.html new file mode 100644 index 0000000..6df0fd4 --- /dev/null +++ b/help/html/features/mmcif.html @@ -0,0 +1,28 @@ + + + + +mmCIF File Format + + + mmCIF File Format +

The mmCIF file format (macromolecular Crystallographic + Information) was developed under the auspices of the International Union of Crystallography (IUCr) to extend the Crystallographic Information + File (CIF) data representation used for describing small molecule + structures and associated diffraction experiments.

+ Merits of mmCIF file format + + + mmCIF file format support for importing 3D structure data from + flat file and EMBL-PDBe via mmCIF was added in Jalview 2.9.1 + + \ No newline at end of file diff --git a/help/html/features/seqmappings.html b/help/html/features/seqmappings.html index ac63c9e..60ac6ab 100644 --- a/help/html/features/seqmappings.html +++ b/help/html/features/seqmappings.html @@ -42,5 +42,7 @@ retrieved by the Sequence Fetcher, and allows sequence features to be mapped directly from Uniprot das sources to their coding region on EMBL sequence records. +

+

In Jalview 2.9.1 SIFTS Mapping was added as a better means for explicitly identifying the coordinates corresponding to a displayed sequence when viewing a PDB structure associated with a sequence

diff --git a/help/html/features/sifts_mapping_output.png b/help/html/features/sifts_mapping_output.png new file mode 100644 index 0000000..3c28b81 Binary files /dev/null and b/help/html/features/sifts_mapping_output.png differ diff --git a/help/html/features/siftsmapping.html b/help/html/features/siftsmapping.html new file mode 100644 index 0000000..c344a20 --- /dev/null +++ b/help/html/features/siftsmapping.html @@ -0,0 +1,45 @@ + + + + +SIFTS Mapping + + + +

SIFTS Mapping

+ +

+ SIFTS (Structure integration with function, taxonomy + and sequences) provides an up-to-date resource for residue-level + mapping between Uniprot and PDB entries. The information is updated and + released weekly simultaneously with the release of new PDB entries. + SIFTS Entries are published as XML files and made publicly available via an FTP + site hosted at the European Bioinformatics Institute. +

+ +

+ At the point of viewing a PDB structure, Jalview downloads a SIFTS file + for the target entry and uses it to accurately map the sequence residues with the + structure residue. Prior to SIFTS integration, Jalview uses Needleman and Wunsch + Alignment algorithm to map sequence residues to structure residues, and that may not + always result to a correct mapping since it is computational determined. +

+ +

+ The default method for 'Sequence ↔ Structure' mapping can be configured + in the Structure tab in the Tools → Preferences dialog box. When 'SIFTS' + is enabled as the default, all mappings between 'Sequence ↔ Structure' is + performed via SIFTS provided that there is a valid SIFTS entry for PDB structure. If no + valid SIFTS resource is available, then the 'Sequence ↔ Structure' mapping falls + back to Needleman and Wunsch Alignment algorithm. +

+ +

To verify the mapping method used, you can view the mapping output via the structure viewer menu File → View mapping. A sample mapping output can be seen in the screenshot below. The highlighted position shows the method used.

+

+ SIFTS mapping output +

+ +

SIFTS Mapping integration was added in Jalview 2.9.1

+ + + \ No newline at end of file diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 4d35516..d4819f1 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -121,6 +121,19 @@

+ Importing PDB Entries or files in mmCIF format
+ mmCIF file format provides an alternative means for + importing 3D structure data from flat file and EMBL-PDBe + web-service. To enable mmCIF as the default format for + importing PBD sequences from the PDB sequence fetcher, add or modify the + property + DEFAULT_STRUCTURE_FORMAT=mmCIF in Jalview properties file. + Once this is done, the steps followed in retrieving PDB format files above can + be followed to obtain the same data with mmCIF. mmCIF format file support was added in Jalview 2.9.1.

+ + + +

Associating a large number of PDB files to sequences in an alignment
It is often the case when working with structure alignments that you will have a directory of PDB 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/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index e567d20..71c8a39 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -407,6 +407,10 @@ public class SequenceFetcher extends JPanel implements Runnable this.add(jPanel2, java.awt.BorderLayout.NORTH); jScrollPane1.getViewport().add(textArea); + /* + * open the database tree + */ + database.waitForInput(); } private void pdbSourceAction() 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); }