Merge branch 'JAL-1161_optimisingAnnotationPanel' into develop

Conflicts:
	src/jalview/datamodel/Annotation.java
	src/jalview/io/AppletFormatAdapter.java
	src/jalview/io/StockholmFile.java
	src/jalview/renderer/AnnotationRenderer.java
Feature conflict left unresolved - JAL-1081 (Pseuodknots) which utilises VARNA to process stockholm annotation data

diff --git a/doc/AnnotationPostAnalysis.txt b/doc/AnnotationPostAnalysis.txt
new file mode 100644 (file)
index 0000000..f53533f
--- /dev/null
+++ b/doc/AnnotationPostAnalysis.txt
@@ -0,0 +1,39 @@
+Init.
+optimise rendering - use same model as alignment but with vertical binary sweep to select range of annotation to render:
+Vertical interval list
+. run length compress the sizes -> n_i * v_height_i -> label each node - total and accumulated total vertical pos (under current visibility settings ?)
+--> ins/delete/hide/show of one or more contiguous individual rows causes local -> global update of position sums.
+--
+. 
+indexOf(VPosition in annotation display window),
+VPositionOf(AnnotationI)
+
+0.
+i. Hide/show by whole annotation set id
+ii. move to top/bottom
+iii. 
+
+1. Summarising annotation
+{ Annotation Class ID 
+|_ { Type string } }
+-> 
+
+Simple modal : 
+- Proportion of sequences with most frequent symbol
+- symbol logo
+[ option to drill down and subselect based on particular symbol or subdivide by all symbols ]
+
+3. Clustering based on annotation
+A few routes:
+use built in PCA calculation to do scalar product based analysis of one or many annotation vectors.
+Sliding window over alignment doing pca at each point. Analyse trajectories through PCA ?  (see maximum/minimum and stretches of local similarity)
+
+
+* ''' ACCESS ALL MENUS '''
+-> allow context popup to show all window submenus
+{ local relevant }
+{ Parent window -> file,edit,etc }
+{ Desktop -> File, Tools, ... }
+{ other areas more distant - e.g. sequence/annotation ID popup from middle of alignment/annotation area }
+ 
+ 
\ No newline at end of file

diff --git a/examples/PF00111_seed.stk b/examples/PF00111_seed.stk
new file mode 100644 (file)
index 0000000..d98c09f
--- /dev/null
+++ b/examples/PF00111_seed.stk
@@ -0,0 +1,523 @@
+# STOCKHOLM 1.0
+#=GF ID   Fer2
+#=GF AC   PF00111.22
+#=GF DE   2Fe-2S iron-sulfur cluster binding domain
+#=GF PI   fer2; 
+#=GF AU   Sonnhammer ELL
+#=GF SE   Prosite
+#=GF GA   20.70 15.00;
+#=GF TC   20.70 15.70;
+#=GF NC   20.60 14.90;
+#=GF BM   hmmbuild HMM.ann SEED.ann
+#=GF SM   hmmsearch -Z 15929002 -E 1000 --cpu 4 HMM pfamseq
+#=GF TP   Domain
+#=GF WK   Ferredoxin
+#=GF DR   INTERPRO; IPR001041;
+#=GF DR   PROSITE; PDOC00175;
+#=GF DR   PROSITE; PDOC00642;
+#=GF DR   SCOP; 3fxc; fa;
+#=GF DR   HOMSTRAD; fer2;
+#=GF DR   HOMSTRAD; Ald_Xan_dh_1;
+#=GF SQ   206
+#=GS FER_GLEJA/8-82        AC P00233.1
+#=GS FER2_RAPSA/9-84       AC P14937.1
+#=GS Q39648_CITSI/61-136   AC Q39648.1
+#=GS FER3_MAIZE/63-138     AC P27788.1
+#=GS FER6_MAIZE/66-141     AC P94044.1
+#=GS FER1_SYNP2/9-83       AC P31965.2
+#=GS FER1_EQUAR/7-81       AC P00235.1
+#=GS FER2_EQUAR/7-80       AC P00237.1
+#=GS FER2_EQUAR/7-80       DR PDB; 1WRI A; 7-80;
+#=GS FER2_PLEBO/10-85      AC P46035.2
+#=GS P95533_PSEPU/253-328  AC P95533.1
+#=GS KSHB_MYCTU/273-348    AC P96853.1
+#=GS Q44253_ACISP/251-326  AC Q44253.1
+#=GS Q59656_PLEBO/573-647  AC Q59656.1
+#=GS P71846_MYCTU/600-675  AC P71846.3
+#=GS O84985_PSEPU/271-347  AC O84985.2
+#=GS PAAE_ECOLI/266-342    AC P76081.1
+#=GS HCR_ECOLI/241-316     AC P75824.3
+#=GS O87803_PSEST/5-82     AC O87803.2
+#=GS TMOF_PSEME/4-81       AC Q03304.1
+#=GS O32476_PSESP/4-81     AC O32476.1
+#=GS Q51944_BURPI/5-82     AC Q51944.1
+#=GS Q53028_RHOCO/4-80     AC Q53028.1
+#=GS Q45344_BURPI/10-88    AC Q45344.1
+#=GS Q9ZNP1_COMTE/9-88     AC Q9ZNP1.1
+#=GS Q9Z418_PSEPU/11-90    AC Q9Z418.1
+#=GS Q9ZAN6_9BURK/12-91    AC Q9ZAN6.1
+#=GS FERN_PSEPU/7-85       AC P23263.1
+#=GS O24827_ACISP/7-85     AC O24827.1
+#=GS FERX_PSEPU/8-86       AC P23103.1
+#=GS Q52061_PSEPU/8-86     AC Q52061.1
+#=GS Q52167_PSEPU/8-86     AC Q52167.1
+#=GS O84964_9RALS/4-82     AC O84964.1
+#=GS Q9Z3W9_9SPHN/8-85     AC Q9Z3W9.1
+#=GS DMPP_PSEUF/5-82       AC P19734.3
+#=GS O84963_9RALS/4-81     AC O84963.1
+#=GS Q52574_PSESP/5-83     AC Q52574.1
+#=GS Q9ZNP2_COMTE/5-82     AC Q9ZNP2.1
+#=GS Q43983_ACICA/5-82     AC Q43983.1
+#=GS O87617_PSEAE/3-78     AC O87617.1
+#=GS O52378_9RALS/3-78     AC O52378.1
+#=GS Q51492_PSEAE/3-78     AC Q51492.1
+#=GS NDOR_PSEPU/3-78       AC Q52126.1
+#=GS Q52140_PSEPU/3-78     AC Q52140.1
+#=GS Q9Z9X8_9GAMM/242-317  AC Q9Z9X8.1
+#=GS VANB_PSEUH/234-309    AC O05617.1
+#=GS VANB_PSES9/231-306    AC P12580.1
+#=GS VANB_PSEPU/231-307    AC O54037.1
+#=GS VANB_ACIAD/234-309    AC O24840.1
+#=GS O88034_STRCO/230-305  AC O88034.1
+#=GS P94680_COMTE/234-309  AC P94680.1
+#=GS CBAB_COMTE/232-307    AC Q44257.2
+#=GS POBB_PSEPS/236-311    AC Q52186.1
+#=GS YEAX_ECOLI/237-313    AC P76254.1
+#=GS Q47914_SPHCR/241-316  AC Q47914.2
+#=GS PDR_BURCE/241-314     AC P33164.3
+#=GS PDR_BURCE/241-314     DR PDB; 2PIA A; 240-313;
+#=GS PHT2_PSEPU/243-316    AC Q05182.1
+#=GS O86347_MYCTU/231-301  AC O86347.3
+#=GS YFAE_ECOLI/4-77       AC P0ABW3.1
+#=GS Y1309_HAEIN/3-75      AC P45154.1
+#=GS O31003_VIBAN/5-73     AC O31003.1
+#=GS RFBI_SALTY/5-76       AC P26395.1
+#=GS P95461_9PSED/17-94    AC P95461.1
+#=GS O85971_SPHAR/13-90    AC O85971.1
+#=GS XYLA_PSEPU/20-97      AC P21394.1
+#=GS YCBX_ECOLI/293-362    AC P75863.1
+#=GS P96096_THIFE/9-86     AC P96096.1
+#=GS MMOC_METTR/7-81       AC Q53563.1
+#=GS O85675_ACIAD/8-85     AC O85675.1
+#=GS BENC_ACIAD/19-98      AC P07771.2
+#=GS BENC_ACIAD/19-98      DR PDB; 1KRH B; 9-88;
+#=GS BENC_ACIAD/19-98      DR PDB; 1KRH A; 9-88;
+#=GS XYLZ_PSEPU/8-86       AC P23101.1
+#=GS CBDC_BURCE/8-85       AC Q51603.1
+#=GS O66892_AQUAE/7-72     AC O66892.1
+#=GS O85226_PSEFL/27-86    AC O85226.1
+#=GS O29575_ARCFU/14-75    AC O29575.1
+#=GS O27878_METTH/21-82    AC O27878.1
+#=GS Y092_METJA/14-73      AC Q57557.1
+#=GS FER5_RHOCA/10-107     AC P37097.2
+#=GS Q44501_AZOVI/10-107   AC Q44501.1
+#=GS Q46508_DESFR/6-74     AC Q46508.1
+#=GS Q9ZBV9_STRCO/15-78    AC Q9ZBV9.1
+#=GS NUOG_MYCTU/19-82      AC P95175.2
+#=GS O87815_CUPNE/22-85    AC O87815.1
+#=GS NQO3_THET8/4-88       AC Q56223.2
+#=GS NQO3_THET8/4-88       DR PDB; 3M9S C; 4-88;
+#=GS NQO3_THET8/4-88       DR PDB; 3M9S 3; 4-88;
+#=GS P74022_SYNY3/6-69     AC P74022.1
+#=GS P94157_SYNP6/6-69     AC P94157.1
+#=GS Q44513_ANAVA/6-69     AC Q44513.1
+#=GS P77908_MOOTH/4-67     AC P77908.3
+#=GS Q9ZJW1_HELPJ/4-65     AC Q9ZJW1.1
+#=GS O05397_BACSU/11-72    AC O05397.1
+#=GS YJGC_BACSU/7-68       AC O34720.1
+#=GS NUOG_SALTI/4-72       AC P0A1Y5.2
+#=GS O66748_AQUAE/6-70     AC O66748.1
+#=GS NDUS1_DICDI/5-71      AC Q34312.1
+#=GS NQO3_PARDE/7-71       AC P29915.4
+#=GS NDUS1_NEUCR/38-101    AC P24918.2
+#=GS NUOG_RICPR/4-67       AC Q9ZCF6.1
+#=GS NDUS1_SOLTU/70-133    AC Q43644.1
+#=GS NDUS1_RECAM/4-67      AC O21241.1
+#=GS NDUS1_BOVIN/34-97     AC P15690.1
+#=GS O52683_THEMA/3-65     AC O52683.1
+#=GS Q46606_DESVU/3-71     AC Q46606.1
+#=GS HOXU_CUPNH/5-66       AC P22318.2
+#=GS P72305_RHOOP/5-66     AC P72305.1
+#=GS Q59261_CLOSA/4-67     AC Q59261.1
+#=GS Q9ZNE4_CLOPE/4-67     AC Q9ZNE4.1
+#=GS PHF1_CLOPA/4-67       AC P29166.1
+#=GS Q59262_CLOAB/4-66     AC Q59262.1
+#=GS P74801_SYNY3/5-63     AC P74801.1
+#=GS XDHE_BACSU/18-77      AC O32143.1
+#=GS HCRC_THAAR/7-66       AC O33818.1
+#=GS HCRC_THAAR/7-66       DR PDB; 1SB3 F; 7-66;
+#=GS HCRC_THAAR/7-66       DR PDB; 1RM6 C; 7-66;
+#=GS HCRC_THAAR/7-66       DR PDB; 1RM6 F; 7-66;
+#=GS HCRC_THAAR/7-66       DR PDB; 1SB3 C; 7-66;
+#=GS P95635_RHOPA/15-74    AC P95635.1
+#=GS XDHC_ECOLI/11-69      AC Q46801.1
+#=GS YAGT_ECOLI/65-124     AC P77165.1
+#=GS DCMS_HYDPS/8-67       AC P19915.2
+#=GS Q52589_9PSED/8-67     AC Q52589.1
+#=GS O52837_BRAJA/6-65     AC O52837.1
+#=GS O53709_MYCTU/5-64     AC O53709.1
+#=GS O87682_ARTNI/8-67     AC O87682.1
+#=GS Q59128_ARTNI/14-73    AC Q59128.1
+#=GS P72223_PSEPU/14-73    AC P72223.1
+#=GS P72223_PSEPU/14-73    DR PDB; 1T3Q A; 14-73;
+#=GS P72223_PSEPU/14-73    DR PDB; 1T3Q D; 14-73;
+#=GS Q9ZBN8_STRCO/5-65     AC Q9ZBN8.1
+#=GS O54050_RHOCA/5-68     AC O54050.1
+#=GS O54050_RHOCA/5-68     DR PDB; 1JRP A; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 2W3R A; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 2W3S A; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 1JRP G; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 2W54 E; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 1JRP E; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 2W55 A; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 2W3R E; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 2W3S E; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 2W54 G; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 2W3R G; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 2W54 A; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 1JRO A; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 1JRO E; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 2W55 E; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 2W55 C; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 2W3R C; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 1JRO C; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 2W54 C; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 2W3S G; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 2W55 G; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 2W3S C; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 1JRO G; 5-68;
+#=GS O54050_RHOCA/5-68     DR PDB; 1JRP C; 5-68;
+#=GS O23887_MAIZE/15-85    AC O23887.1
+#=GS ALDO4_ARATH/8-78      AC Q7G191.2
+#=GS ALDO1_ARATH/23-95     AC Q7G193.2
+#=GS O30328_ACEEU/4-63     AC O30328.1
+#=GS IORA_BREDI/4-64       AC Q51697.1
+#=GS XDH_EMENI/39-108      AC Q12553.2
+#=GS O61198_CAEEL/8-78     AC O61198.2
+#=GS O17892_CAEEL/18-86    AC O17892.1
+#=GS XDH_DROSU/13-83       AC P91711.1
+#=GS O17506_BOMMO/19-89    AC O17506.1
+#=GS Q17250_BOMMO/18-88    AC Q17250.2
+#=GS ADO_BOVIN/9-79        AC P48034.2
+#=GS XDH_BOVIN/8-78        AC P80457.4
+#=GS XDH_BOVIN/8-78        DR PDB; 1V97 B; 8-78;
+#=GS XDH_BOVIN/8-78        DR PDB; 3NVY A; 8-78;
+#=GS XDH_BOVIN/8-78        DR PDB; 3NVY J; 8-78;
+#=GS XDH_BOVIN/8-78        DR PDB; 3NRZ J; 8-78;
+#=GS XDH_BOVIN/8-78        DR PDB; 3NVV A; 8-78;
+#=GS XDH_BOVIN/8-78        DR PDB; 3NRZ A; 8-78;
+#=GS XDH_BOVIN/8-78        DR PDB; 1N5X A; 8-78;
+#=GS XDH_BOVIN/8-78        DR PDB; 1N5X B; 8-78;
+#=GS XDH_BOVIN/8-78        DR PDB; 1V97 A; 8-78;
+#=GS XDH_BOVIN/8-78        DR PDB; 1VDV A; 8-78;
+#=GS XDH_BOVIN/8-78        DR PDB; 3NVV J; 8-78;
+#=GS XDH_BOVIN/8-78        DR PDB; 1VDV B; 8-78;
+#=GS XDH_BOVIN/8-78        DR PDB; 3NS1 A; 8-78;
+#=GS XDH_BOVIN/8-78        DR PDB; 3NS1 J; 8-78;
+#=GS MOP_DESGI/6-65        AC Q46509.1
+#=GS MOP_DESGI/6-65        DR PDB; 1VLB A; 6-65;
+#=GS MOP_DESGI/6-65        DR PDB; 1SIJ A; 6-65;
+#=GS O53669_MYCTU/13-78    AC O53669.1
+#=GS O29566_ARCFU/5-80     AC O29566.1
+#=GS O30225_ARCFU/5-84     AC O30225.1
+#=GS NQRF_CHLTR/46-122     AC O84745.1
+#=GS NQRF_HAEIN/43-119     AC O05012.1
+#=GS NQRF_VIBAL/39-115     AC Q56584.1
+#=GS O84062_CHLTR/8-83     AC O84062.1
+#=GS Q9Z8H9_CHLPN/8-83     AC Q9Z8H9.1
+#=GS CSMJ_CHLTE/5-82       AC O68983.1
+#=GS CSMI_CHLTE/5-82       AC O68988.1
+#=GS FER_TRIVA/13-90       AC P21149.1
+#=GS FER_TRIVA/13-90       DR PDB; 1L5P A; 5-83;
+#=GS FER_TRIVA/13-90       DR PDB; 1L5P C; 5-83;
+#=GS FER_TRIVA/13-90       DR PDB; 1L5P B; 5-83;
+#=GS P73774_SYNY3/7-88     AC P73774.1
+#=GS FER_BUCAP/10-92       AC O51882.1
+#=GS O69222_AZOVI/11-93    AC O69222.1
+#=GS FER_HAEIN/10-92       AC P44428.2
+#=GS FER_PSEAE/10-92       AC Q51383.2
+#=GS ADRX_YEAST/67-149     AC Q12184.1
+#=GS ADX_PIG/71-155        AC P00258.2
+#=GS FER2_RICPR/11-93      AC Q9ZDW6.1
+#=GS O49551_ARATH/44-127   AC O49551.1
+#=GS ETP1_SCHPO/525-592    AC Q10361.2
+#=GS ETP1_SCHPO/525-592    DR PDB; 2WLB A; 525-607;
+#=GS ETP1_SCHPO/525-592    DR PDB; 2WLB B; 525-607;
+#=GS O07876_SPHSX/8-91     AC O07876.1
+#=GS Q9ZAM5_SPHSX/8-91     AC Q9ZAM5.1
+#=GS FER2_CAUCR/8-91       AC P37098.1
+#=GS FER6_RHOCA/7-91       AC P80306.1
+#=GS FER6_RHOCA/7-91       DR PDB; 1UWM A; 7-91;
+#=GS P74447_SYNY3/31-113   AC P74447.1
+#=GS P73171_SYNY3/7-85     AC P73171.1
+#=GS FER1_AQUAE/3-83       AC O67065.1
+#=GS FER4_RHOCA/7-86       AC P16022.1
+#=GS P74283_SYNY3/5-88     AC P74283.1
+#=GS PUTX_PSEPU/8-92       AC P00259.3
+#=GS PUTX_PSEPU/8-92       DR PDB; 1PDX A; 7-91;
+#=GS PUTX_PSEPU/8-92       DR PDB; 1OQR C; 7-91;
+#=GS PUTX_PSEPU/8-92       DR PDB; 1OQR B; 7-91;
+#=GS PUTX_PSEPU/8-92       DR PDB; 1XLP C; 7-91;
+#=GS PUTX_PSEPU/8-92       DR PDB; 1R7S A; 7-91;
+#=GS PUTX_PSEPU/8-92       DR PDB; 1OQR A; 7-91;
+#=GS PUTX_PSEPU/8-92       DR PDB; 1YJJ A; 7-91;
+#=GS PUTX_PSEPU/8-92       DR PDB; 1R7S C; 7-91;
+#=GS PUTX_PSEPU/8-92       DR PDB; 1OQQ B; 7-91;
+#=GS PUTX_PSEPU/8-92       DR PDB; 1XLP A; 7-91;
+#=GS PUTX_PSEPU/8-92       DR PDB; 1XLP B; 7-91;
+#=GS PUTX_PSEPU/8-92       DR PDB; 1R7S B; 7-91;
+#=GS PUTX_PSEPU/8-92       DR PDB; 1OQQ A; 7-91;
+#=GS PUTX_PSEPU/8-92       DR PDB; 1XLN B; 7-91;
+#=GS PUTX_PSEPU/8-92       DR PDB; 1YJI A; 7-91;
+#=GS PUTX_PSEPU/8-92       DR PDB; 1XLN A; 7-91;
+#=GS TERPB_PSESP/8-92      AC P33007.2
+#=GS P95277_MYCTU/9-84     AC P95277.1
+#=GS O05933_PSEPU/11-88    AC O05933.1
+#=GS DESET_MYCTU/303-373   AC O05875.1
+#=GS O23344_ARATH/57-131   AC O23344.1
+#=GS P74159_SYNY3/11-86    AC P74159.1
+#=GS FER2_SYNP6/8-83       AC P08451.2
+#=GS P73388_SYNY3/9-84     AC P73388.1
+#=GS FER1_HALMA/35-108     AC P00217.2
+#=GS P74449_SYNY3/11-88    AC P74449.1
+#=GS FER2_NOSMU/10-85      AC P00249.2
+#=GS FER2_APHSA/10-86      AC P00251.2
+#=GS FER1_CYAPA/10-85      AC P17007.3
+#=GS FER_PORPU/10-85       AC P51320.2
+#=GS FER_ODOSI/10-85       AC P49522.2
+#=GS FER_BUMFI/9-84        AC P13106.1
+#=GS FER3_CYACA/9-84       AC P00241.1
+#=GS FER2_CYACA/8-83       AC P15789.1
+#=GS FER_BRYMA/8-83        AC P07838.1
+#=GS FER_APHSA/9-83        AC P00250.2
+#=GS FER_THEVL/9-84        AC P0A3D1.2
+#=GS FER_PERBI/6-80        AC P10770.1
+#=GS FER3_RAPSA/8-82       AC P14938.1
+#=GS FER1_SPIOL/58-132     AC P00221.2
+#=GS FER_SILPR/57-131      AC P04669.1
+#=GS FER_WHEAT/54-128      AC P00228.2
+#=GS FER_SAMNI/8-82        AC P00226.1
+#=GS FERA_ALOMA/8-82       AC P81372.1
+#=GS FER_ARCLA/8-82        AC P00223.1
+#=GS FER_DATST/8-82        AC P68165.1
+#=GS FER_PALPL/9-83        AC P07484.1
+#=GS FER_EUGVI/8-82        AC P22341.1
+#=GS FER_CHLFU/6-80        AC P56408.1
+#=GS FER_SYNY4/9-83        AC P00243.2
+#=GS FER1_PHYAM/8-82       AC P00229.1
+#=GS FER2_PHYAM/9-83       AC P00231.1
+#=GS FER2_SPIOL/8-82       AC P00224.1
+#=GS FER_PHYPA/57-132      AC O04166.1
+#=GS FER_MARPO/7-81        AC P09735.1
+FER_GLEJA/8-82                   LTPDGE...RTIEVPDDKF.ILDAGE...E.A.GLDLPYSCRA.......GA....CSSCTGKLLDGRV.....DQSE...QSFLDDDQMAEGFV.....................LTCVAYPA
+FER2_RAPSA/9-84                  IGPEGE..ENEFEVQDDQF.ILDAAE...E.A.GVDLPYSCRA.......GA....CSTCAGQIVKGQV.....DQSE...GSFLEDDHFEKGFV.....................LTCVAYPQ
+Q39648_CITSI/61-136              IGPMGE..EHEFEAQEDQY.ILDAAE...E.A.GVDLPYSCRA.......GA....CSTCAGKLVSGSV.....DQSD...GSFLDDNQMEAGYL.....................LTCISYPT
+FER3_MAIZE/63-138                VGPEGE..EHEFDAPDDAY.ILDAAE...T.A.GVELPYSCRA.......GA....CSTCAGKIESGSV.....DQSD...GSFLDDGQQEEGYV.....................LTCVSYPK
+FER6_MAIZE/66-141                VGPDGT..EHEFEAPDDTY.ILEAAE...T.A.GVELPFSCRA.......GS....CSTCAGRMSAGEV.....DQSE...GSFLDDGQMAEGYL.....................LTCISYPK
+FER1_SYNP2/9-83                  ITPDGE...VSYDAPDDEY.ILDSAG...D.A.GYDLPASCRA.......GA....CSTCAGKIVSGTV.....DQSE...QSFLDDDQIEAGYV.....................LTCIAYPQ
+FER1_EQUAR/7-81                  KTPSGE...FTLDVPEGTT.ILDAAE...E.A.GYDLPFSCRA.......GA....CSSCLGKVVSGSV.....DESE...GSFLDDGQMEEGFV.....................LTCIAIPE
+FER2_EQUAR/7-80                  KTPDGD...ITFDVEPGER.LIDIGS...E.K..ADLPLSCQA.......GA....CSTCLGKIVSGTV.....DQSE...GSFLDDEQIEQGYV.....................LTCIAIPE
+#=GR FER2_EQUAR/7-80       SS    E-----...EEEEE-----.TT----...-.S..S----SS--.......--....-STT---EEE-EE.....E---...-----HHHHH----.....................-TTT-EEE
+FER2_PLEBO/10-85                 NKKRNL..DITLPVDEDTT.VLEAAE...E.A.ELDLPFSCHS.......GA....CSSCVGKVVEGEI.....NQDD...QTFLDEEQVAKGFV.....................LLCVTYPR
+P95533_PSEPU/253-328             VLMKGQ..THAVPVRAGEL.LLSAML...R.A.GLPAPHACRV.......GE....CASCMCRLQAGEVQ....RLDS....SVLDEDDVAAG.W...................L.LACRTRAA
+KSHB_MYCTU/273-348               VELDGQ..THTVSWPRTAK.LLDVLL...A.A.GLDAPFSCRE.......GH....CGACACTLRAGKVN....MGVN....DVLEQQDLDEG.L...................I.LACQSRPE
+Q44253_ACISP/251-326             FMLNGI..KNSVMCSEDDFILNEIIK......AGINVPSSCCA.......GN....CGSCMCLLVSGDVI....LESN....TVLDASDEEDGWI.....................LACRSKPR
+Q59656_PLEBO/573-647             FAQSGK....EITCTQDDL.ILDIAD.....QAEVAIESSCRS.......GT....CGSCKCTLLEGEV.....SYDS..EPDVLDEHDRASGQI.....................LTCIARPV
+P71846_MYCTU/600-675             FTLSGQ..RAIFDLVPGDS.ILEGAL...G..LRSDAPYACMG.......GA....CGTCRAKLIEGNVE....MD....HNFALRKAELDAGYI.....................LTCQSHPT
+O84985_PSEPU/271-347             VISDGR..ALTFDLPRNTQNVLDAGN...A.I.GAELPYSCKA.......GV....CSTCKCRVIEGEV.....EMDS...NHALEDYEVAAGYV.....................LSCQTYPV
+PAAE_ECOLI/266-342               VRQDGR..DREIVLNADDESILDAAL...R.Q.GADLPYACKG.......GV....CATCKCKVLRGKV.....AMET...NYSLEPDELAAGYV.....................LSCQALPL
+HCR_ECOLI/241-316                FTKLQP..AREFYAPVGTT.LLEALE.....SNNVPVVAACRA.......GV....CGCCKTKVVSGEY.....TVSS...TMTLTDAEIAEGYV.....................LACSCHPQ
+O87803_PSEST/5-82                IKIADT..DVEFTISDRDT.ILRAAL...R.D.GIPISYECNS.......GG....CGSCKIDVVEGQVE...TLWGE...APGLSPRDKRK.SR...................K.LACQCLAS
+TMOF_PSEME/4-81                  IQSDDL..LHHFEADSNDT.LLSAAL...R.A.ELVFPYECNS.......GG....CGACKIELLEGEVS...NLWPD...APGLAARELRK.NR...................F.LACQCKPL
+O32476_PSESP/4-81                LKIEGQ..APGTCG.SGKS.LLVSAL...A.N.GIGFPYECAS.......GG....CGVCKFELLEGNVQ...SMWPD...APGLSSRDREKGNR...................H.LACQCVAL
+Q51944_BURPI/5-82                ITIEGG..SAFSVAADEDT.LLRGAL...R.G.GIALPHECSV.......GG....CGACRFDLLSGLVE...SIWPE...APGLSERDRKR.GK...................H.LACQSRPL
+Q53028_RHOCO/4-80                INVQPF..SHEYSCEDGES.LLDGAL..RN...SLLLKYGCKH.......GG....CGTCKVRLLDGDV.....EEPG..SSFALTPEDRENDVI.....................LACASVPL
+Q45344_BURPI/10-88               YAWNRP..RSTTHARPPKA.SLTGML...R.LGRKGIPVGCVN.......GG....CGVCKVRVLDGST......RLGR.RQPCPRQRRRRSAGL...................T.LACREAPL
+Q9ZNP1_COMTE/9-88                VSVEQT..GDTYACGTHES.LLSGML...R.LGRKGIPVGCVN.......GG....CGVCKVQVLEGAV.....RHLGP.VSCAHVSDLERDQGY...................T.LACRVAPL
+Q9Z418_PSEPU/11-90               VHVMQT..GETFPCATDES.LLQGML...R.LGRKGIPVGCVN.......GG....CGVCKVHVIEGQC.....RPLGP.VSRAHVSAAEEARGF...................T.LACRVAPV
+Q9ZAN6_9BURK/12-91               VHVAQT..DETFPCAGNES.LLTGMV...R.LGRKGIPVGCVN.......GG....CGVCKVRIVEGQI.....KALGP.ISRAHVTLDEENQGY...................T.LACRVAPQ
+FERN_PSEPU/7-85                  ITVQPG..GERFVCQPQQS.ALHAME...T.QGKRCLPVGCRG.......GG....CGLCKVRVLAGDY......ESGR.VSCKHLPVEAREQGY...................A.LACRLFAR
+O24827_ACISP/7-85                ITEQCS..GQRFPCKAGQS.VLKAME...Q.QGLECAPVGCRG.......GG....CGLCKVTVREGDY......ECGK.MSRVHAPPEALAQGE...................V.LACRIYPL
+FERX_PSEPU/8-86                  VFEVLS..GQSFRCAEGQS.VLRAME...A.QGKRCIPVGCRG.......GG....CGLCRVRVLSGAY......RSGR.MSRGHVPAKAAAEAL...................A.LACQVFPQ
+Q52061_PSEPU/8-86                IRETVS..GQTFRCLPDQS.VLSAME...Q.QGKRCVPVGCRG.......GG....CGLCKVRVLSGTY......QCHK.MSCNHVPPEAAKQGL...................A.LACQLFPQ
+Q52167_PSEPU/8-86                VHETNS..GQSFTCRPDQS.VLRAME...E.QGKRCVPVGCRG.......GG....CGLCKVRVLSGDY......QCGR.MSCSQVPPEAAQQGL...................A.LACQLYPR
+O84964_9RALS/4-82                VEIADS..GQRYPCDPGQN.LLRAME...V.LGQRGIPAGCRG.......GG....CGVCKVRIESGRY......RTGK.MSRACLSEAEQGQGL...................V.LACKAFPD
+Q9Z3W9_9SPHN/8-85                IRILGG..GQ.FACPEGER.VLIAME...Q.FGSSDIGVGCRG.......GG....CGFCLVRVVEGEY......RTGK.MSTAKVSVADQAKGY...................A.LACRIYPM
+DMPP_PSEUF/5-82                  VTIEPT..GEVIEVEDGQT.ILQAAL...R.Q.GVWLPFACGH.......GT....CATCKVQVVEGEVD...IGEAS...PFALMDIERDERKV.....................LACCAIPL
+O84963_9RALS/4-81                LTIEPI..GQTIPIAPGQT.VLDACL...R.S.GVWLPHACCH.......GL....CATCKVQVVEGEVD...QGEAS..SFALMDFER.DNGQC.....................LACCATAQ
+Q52574_PSESP/5-83                LTIEPL..GRTLDVAEGQT.LLDAAL...R.S.GVYIPHACGH.......GL....CGTCKVQVTSGEVD...HGAAN..PLRRSWISSGEEGKT.....................LACCATAL
+Q9ZNP2_COMTE/5-82                LTLEPL..GASIEVEEGQT.LLDAAL...R.Q.GIYIPHACGH.......GL....CGTCKIQVCDGDVD...HGAAN..PFALMDMER.EDGMT.....................LACCATLQ
+Q43983_ACICA/5-82                VTIEPA..GTIIQVEEDQT.ILDAAL...R.Q.GVWLPFACGH.......GT....CGTCKVQVTDGFYD...VGEAS..PFALMDIER.EENKV.....................LACCCKPE
+O87617_PSEAE/3-78                LHIQPL..GQTLSVDSGAN.LLEALR...A.AE.VPISYSCMA.......GR....CGTCRCKVLKGQV......L..E.SGREATLTNPHADDY...................V.LACMSAIT
+O52378_9RALS/3-78                LVVEPL..NLHLNAETGST.LLDVLR...S.NE.VPISYSCMS.......GR....CGTCRCRVIAGHL......R..D.NGPETGRPQAGKGTY...................V.LACQAVLT
+Q51492_PSEAE/3-78                LLVLPN..NRRLPFDSGAN.LLEVLR...E.HR.VGISYSCMS.......GR....CGTCRCRVIDGSV......I..S.SAAKSGDSNRIEEHY...................V.LACQSVLT
+NDOR_PSEPU/3-78                  LLIQPN..NRIIPFSAGAN.LLEVLR...E.NG.VAISYSCLS.......GR....CGTCRCRVIDGSV......I..D.SGAENGQSNLTDKQY...................V.LACQSVLT
+Q52140_PSEPU/3-78                LLIQPN..NRLISFSPGAN.LLEVLR...E.NG.VAISYSCMS.......GR....CGTCRCRVTDGSV......I..D.SGTGSGLPHLVDEHY...................V.LACRSVLT
+Q9Z9X8_9GAMM/242-317             VRIASS..GATVHVDKHTT.IVAALA...S.I.GIEVDTSCGE.......GV....CGTCMVDVVSGTP.....EHRD....HCLSKAERASGKV...................I.CCCVSRAR
+VANB_PSEUH/234-309               VRIHST..GQVLQVPADQT.VSQVLD...A.A.GIIVPVSCEQ.......GI....CGTCITRVVDGEP.....DHRD....FFLTDAEKAKNDQ...................F.TPCCSRAK
+VANB_PSES9/231-306               GRLARS..GLTLQVPAERS.VAQVLD...D.A.GVCIPLACEQ.......GI....CGTCLTRVLDGEP.....EHRD....SFLTDAERARNDQ...................F.TPCCSRAR
+VANB_PSEPU/231-307               VQLNST..GQVFEVPADQS.VVHVLE...Q.H.GIAIAMSCEQ.......GI....CGTCLTRVLSGTPE....ASRP....VFLTEQEQALNDQ...................F.TPCCSRSK
+VANB_ACIAD/234-309               IEVLGS..DRKIEVSAHQT.ATQALL...E.H.GFDVPVSCEQ.......GI....CGTCITRVVSGTP.....DHRD....VFMTDEEHALNDQ...................F.TPCCSRAK
+O88034_STRCO/230-305             VVLARS..GRTVAVPPGTS.VLDAVR...E.T.GVEVLYSCTE.......GT....CGTCETEVVEGEP.....DHRD....SVLTEEERAAGET...................M.LICVSRCR
+P94680_COMTE/234-309             LVLQRA..GLSTTVDAHES.VLDAME...R.V.GVDFPWSCRE.......GI....CGTCEAPVLEGEV.....QHLD....YVLSPEERAEQRR...................M.MVCVSRCG
+CBAB_COMTE/232-307               VNLARS..GAQYVVREGET.ILDVLR...N.A.GHHVTSSCRQ.......GI....CGMCETTLISGVP.....DHRD....RLLTDSEKASGRT...................M.LICCSRAL
+POBB_PSEPS/236-311               VHLARS..GRTIPIAAGCT.ILDALQ...A.G.GVAVPSSCQQ.......GV....CGICETAVLAGVP.....DHRD....LVLSDQERAAGRT...................M.MICCSGSK
+YEAX_ECOLI/237-313               LVLARS..GKEFVVPEEMT.ILQVIE...N.NKAAKVECLCRE.......GV....CGTCETAILEGEA.....DHRD....QYFSDEERASQQS...................M.LICCSRAK
+Q47914_SPHCR/241-316             VLARRS..GQEFTVEPGMT.ILETLL...Q.N.GISRNYSCTQ.......GV....CGTCETKVLEGEP.....DHRD....WVLSDEKKASNST...................M.LICCSLSK
+PDR_BURCE/241-314                VRLSRS..GTSFEIPANRS.ILEVLR...D.A.NVRVPSSCES.......GT....CGSCKTALCSGEA.....DHRD....MVLRDD..EKGTQ...................I.MVCVSRAK
+#=GR PDR_BURCE/241-314     SS    EEES--..--EEEE-TTS-.HHHHHH...H.T.T-----S---.......--....----EEEEEE--E.....E---....SS--TT..T---E...................E.ETTT-EES
+PHT2_PSEPU/243-316               VTLGRS..GIDLEIPVDRS.ILEVLR...D.N.GIRAPSSCES.......GT....CGSCRTRLIEGDV.....EHRD....MVLREDEQH..DQ...................I.MICVSRAR
+O86347_MYCTU/231-301             LELARS..RRVLRVPANRS.ALDVML.....DWDPTTAYSCQQ.......GF....CGTCKVRVLAGQV.....DRRG....RIIEGDN.....E...................M.LVCVSRAV
+YFAE_ECOLI/4-77                  VTLRIT..GTQLLCQDEHP.SLLAAL...E.SHNVAVEYQCRE.......GY....CGSCRTRLVAGQV......D......WIAEPLAFIQPGE...................I.LPCCCRAK
+Y1309_HAEIN/3-75                 IHLIRH..NTTLEFNNET..SLLDHL...E.KNNIHHEYQCRS.......GY....CGSCRVKIKKGKV......S......YKEMPLAFIQPDE...................I.LLCCCHVE
+O31003_VIBAN/5-73                VIVKPS..GVEYQSG..RN.ILDDAF...A.S.SISLEHSCKT.......GD....CGVCCAEVISGLV.....ENEN........GELVTQG.H...................I.LTCQSKAK
+RFBI_SALTY/5-76                  IKIFPS..NIEFSGREDES.ILDAAL...S.A.GIHLEHSCKA.......GD....CGICESDLLAGEVV....DSKG.........NIFGQGDK...................I.LTCCCKPK
+P95461_9PSED/17-94               VQILPQ..DVTIVLEPGQT.LLEAAL...A.N.GIAYPHDCTV.......GT....CASCKTRLKQGRVR...EATPF...GYTLSKAELDA.GY...................I.LACQAFPR
+O85971_SPHAR/13-90               VTVEGS..PTTLDIPAGKT.LLEAML...D.A.GLAMPHDCKV.......GS....CGTCKFKLVSGKIG...ELSPS...ALALEGDELRS.GF...................R.LACQAIPR
+XYLA_PSEPU/20-97                 VSVRGQ..GFQFKVPRGQT.ILESAL...H.Q.GIAFPHDCKV.......GS....CGTCKYKLISGRVN...ELTSS...AMGLSGDLYQS.GY...................R.LGCQCIPK
+YCBX_ECOLI/293-362               IDWQGQ....AFRGNNQQV.LLEQLE.....NQGIRIPYSCRA.......GI....CGSCRVQLLEGEV......T.P......LKKSAMGDDGT....................ILCCSCVPK
+P96096_THIFE/9-86                HTRDKQ..QVSFVCSEAED.LLSAAD...R.G.SILLPSQCRK.......GT....CGACVATVTAGTYH...LGEVS..MEALPEKAQ.ARGDV.....................LLCRTYPR
+MMOC_METTR/7-81                  ETEDGE..TCRRMR.PSED.WISR.A...E.A.ERNLLASCRA.......G.....CATCKADCTDGDYE...LIDVK..VQAVPPDEE.EDGKV.....................LLCRTFPR
+O85675_ACIAD/8-85                NFADGK..TFFIAVQEDEL.LLDAAV...R.Q.GINLPLDCRE.......GV....CGTCQGTCETGIYE...QEYVD..EDALSERDL.AKRKM.....................LACQTRVK
+BENC_ACIAD/19-98                 QFEDGV..TRFIRIAQGET.LSDAAY...R.Q.QINIPMDCRE.......GA....CGTCRAFCESGNYD...MPEDNY.IEDALTPEEAQQGYV.....................LACQCRPT
+#=GR BENC_ACIAD/19-98      SS    E-----..EEEEEE-----.HHHHHH...H.T.T---S-S---.......--....----EEEEEE-EEE...--GGGS.-TTT--HHHHH---E.....................ETTT-EEE
+XYLZ_PSEPU/8-86                  DFEDGV..TRFIDANTGET.VADAAY...R.Q.GINLPLDCRD.......GA....CGACKCFAESGRYS...LGEE.YIEDALSEAEA.EQGYV.....................LTCQMRAE
+CBDC_BURCE/8-85                  RFEDDV..TYFITSSEHET.VADAAY...Q.H.GIRIPLDCRN.......GV....CGTCKGFCEHGEYD...GGDY.I.EDALSADEA.REGFV.....................LPCQMQAR
+O66892_AQUAE/7-72                RYSDGDFRWEEYEVDGEGKTVLEILQNIKEIDPTLSFRAMCRA.......GI....CGTCVVKVN.....................GEHK..........................LACNTRVY
+O85226_PSEFL/27-86               VTA.AL..GETVLSVIQATGLRQVAR...N.DHGQLVGAYCGM.......GV....CHCCLVQIDG...................RHKR...........................RACQTLVK
+O29575_ARCFU/14-75               AYWQSFEVPAKR.GMTVLEALYYIKE...NLDSSLAFRASCRM.......GI....CGSCAMKIN.....................DKP..........................RLACETQVL
+O27878_METTH/21-82               PHLESYEIPSKE.KMKVLDALQLINK...IHGANIAFRSSCRA.......GQ....CGSCAVKMN.....................GEV..........................VLACRAEVE
+Y092_METJA/14-73                 EYLESYEVP..E.NITVLEALEYINK...HYEANILFRASCRN.......AQ....CGSCAVTIN.....................GEP..........................RLACETKVE
+FER5_RHOCA/10-107                IMKKDK..TIYAVAGNTATILALAKE...H.AIPIPF..ECG........DG...DCASCLIEVTHLDN.....KPAMAMMLTEKEKARLKELQMITAEEIEAA..EVSDLPPRFRLACQFIPR
+Q44501_AZOVI/10-107              LMPHNK..KVQAVAGKRSTLLGVAQE...N.GVKIPF..ECQ........DG...NCGSCLVKITHLDG.....ERIKGMLLTDKERNVLKSVGKLPKSEEERA..AVRDLPPTYRLACQTIVT
+Q46508_DESFR/6-74                ITIDGK..TTSVPE...GSTILDAAK...T.L.DIDIPTLCYLNLEALSINNKAASCRVCVVE.....................VEGRRN....L....................APSCATPVT
+Q9ZBV9_STRCO/15-78               FTLDGQ..EARVPE...GSTILDACR...A.A.GKDVPTLCEGDT..LAPKN...ACRVCVVD.....................VEGART....L....................APACSRKAE
+NUOG_MYCTU/19-82                 LTIDGV..EISVPK...GTLVIRAAE...L.M.GIQIPRFCDHPL..LEPVG...ACRQCLV.....................EVEGQR....KP....................LASCTTVAT
+O87815_CUPNE/22-85               LEVDGV..SVTVPA...GTSVMRAAM...E.A.QIAVPKLCATDS..LRNFG...SCRLCLV.....................EIEGRR....GY....................PASCTTPVE
+NQO3_THET8/4-88                  VKVNDR..IVEVPP...GTSVMDAVF...H.A.GYDVPLFCSEKH..LSPIG...ACRMCLVRIGLPKKGPDGKPLLNEKGEPEIQWQP....KL....................AASCVTAVA
+#=GR NQO3_THET8/4-88       SS    EE-SS-..EEEE--...--BHHHHHH...H.-.------SS--TT..S----...----SEEB-------------------------S....S-....................EETTT-B--
+P74022_SYNY3/6-69                LTIDDK..AIAIEE...GASILQAAK...E.A.GVPIPTLCHLEG..ISEAA...ACRLCMVE.....................VEGTNK....L....................MPACVTAVS
+P94157_SYNP6/6-69                LQIDDQ..ELAANV...GQTVLQVAR...E.A.SIPIPTLCHLQG..VSDVG...ACRLCVVE.....................VAGSPK....L....................QPACLLTVS
+Q44513_ANAVA/6-69                LTINDQ..LISAQE...EETLLQAAQ...E.A.GIHIPTLCHLEG..VGDVG...ACRLCLVE.....................VAGSNK....L....................LPACVTKVA
+P77908_MOOTH/4-67                LTIDGQ..RVTAPE...GMTILEVAR...E.N.GIHIPTLCHHPK..LRPLG...YCRLCLVD.....................IEGAAK....P....................MTACNTPVA
+Q9ZJW1_HELPJ/4-65                MNINGK..TIECQE...GQSVLEAAR...S.A.GIYIPTICYLSG..CSPTV...ACKMCMV........................EMDG...KR....................IYSCNTKAK
+O05397_BACSU/11-72               VRVDGT..EIQARA...GATILDILN...E.N.GIEYPQICHVPE..VDPIQ...TCDTCIV........................EANG...KL....................VRSCATVAE
+YJGC_BACSU/7-68                  ITINGV..EMEASE...EQTVLQLLN...N.S.SIEVPQVCYHPS..LGPIE...TCDTCIV........................SING...EL....................KRSCSAELK
+NUOG_SALTI/4-72                  IHVDGK....EYEVNGADN.LLQACL...S.L.GLDIPYFCWHPAL.GSVGA....CRQCAVK..................QYQNAEDTR...GR...................LVMSCMTPAT
+O66748_AQUAE/6-70                KIYIDD...VEIEAEKGKTVLQVALE..N....GIDIPYFCYHPR..LSIAG...ACRMCVVY.......................WEDINR......................LVISCNLPVQ
+NDUS1_DICDI/5-71                 FKINEI..ECEVNEEKEDITILQACT...A.N.GIEIPRFCYHEK..LTIAG...NCRMCLV.....................YVTNEE....KL....................LAACGIPLD
+NQO3_PARDE/7-71                  IKIDDT....IIEVDPNMT.LIQACE...M.A.GIEVPRFCYHER..LSIAG...NCRMCLVEVVGG........PPK........PA............................ASCAMQVK
+NDUS1_NEUCR/38-101               LTIDGK..KVSIEA...GSALIQACE...K.A.GVTIPRYCYHEK..LMIAG...NCRMCLV.....................EVEKVP....KP....................VASCAWPVQ
+NUOG_RICPR/4-67                  LIIDGS..EIEISE...GSTVYQACI...Q.A.GKEIPHFCYHAR..LKIAG...NCRMCLV.....................EIEKSQ....KP....................VASCAMPVS
+NDUS1_SOLTU/70-133               VFVDGY..PVKIPK...GMTVLQACE...I.A.GVDIPRFCYHSR..LSIAG...NCRMCLV.....................EVEKSP....KP....................VASCAMPAL
+NDUS1_RECAM/4-67                 VFVDGL..SVEVKK...GATILQACA...Q.V.GIEIPRFCYHER..LSIAG...NCRMCLV.....................EVEKSP....KP....................VASCAMPVM
+NDUS1_BOVIN/34-97                VFVDGQ..SVMVEP...GTTVLQACE...K.V.GMQIPRFCYHER..LSVAG...NCRMCLV.....................EIEKAP....KV....................VAACAMPVM
+O52683_THEMA/3-65                IYVDGR..EVIIN..DNERNLLEALK.....NVGIEIPNLCYLS.....EASIYGACRMCLVEIN.......................GQIT........................TSCTLKPY
+Q46606_DESVU/3-71                AFINGK..EVRCEP...GRTILEAAR...E.N.GHFIPTLCELADIGHAPGT....CRVCLVE.....................IWRDKEAGPQI....................VTSCTTPVE
+HOXU_CUPNH/5-66                  ITIDGK..TLTTEE...GRTLVDVAA...E.N.GVYIPTLCYLKDK.PCLGT....CRVCSVKVN.....................GN......V....................AAACTVRVS
+P72305_RHOOP/5-66                IEIDGV..TVTTEE...SRTLVDVAA...E.A.GVYIPTLCYLKGK.PSLGT....CRVCSVK.....................LNGTV..........................VAACTIRVA
+Q59261_CLOSA/4-67                IVIDEK..TIQVQE...NTTVIQAAL...A.N.GIDIPSLCYLNEC.GNVGK....CGVCAVE.....................IEGKNN....L....................ALACITKVE
+Q9ZNE4_CLOPE/4-67                IIINDK..TIEFDG...DKTILDLAR...E.N.GFDIPVLCELKNC.GNKGQ....CGVCLVE.....................QEGNDR....L....................LRSCAIKAK
+PHF1_CLOPA/4-67                  IIINGV..QFNTDE...DTTILKFAR...D.N.NIDISALCFLNNCNNDINK....CEICTVE.....................VEGTG.....L....................VTACDTLIE
+Q59262_CLOAB/4-66                IILNGN..EVHTDK...DITILELAR...E.N.NVDIPTLCFLKDC.GNFGK....CGVCMVE.....................VEGKG.....F....................RAACVAKVE
+P74801_SYNY3/5-63                IHFLPD..DVTVAARVGEPILDVAER......AGVFIPTGCLM.......GS....CHACEVELG.......................DGTP.......................ICACISAVP
+XDHE_BACSU/18-77                 MTVNGQ..AWEV.AAVPTTHLSDLLR...KEFQLTGTKVSCGI.......GR....CGACSILID.....................GK......L....................ANACMTMAY
+HCRC_THAAR/7-66                  LTLNGR..ARED.LVPDNMLLLDYLR...ETVGLTGTKQGCDG.......GE....CGACTVLVD.....................DR......P....................RLACSTLAH
+#=GR HCRC_THAAR/7-66       SS    EEE---..EEEE.EEETT-BHHHHHH...HT------------.......--....----EEEET.....................TE......E....................EEGGGSBGG
+P95635_RHOPA/15-74               LNVNGR..WRED.AVTDDMLLVDYLR...DIAGLTGVKTGCDG.......GE....CGACTVLID.....................GE......A....................APSCLVLAV
+XDHC_ECOLI/11-69                 CTINGM..PFQLHAAPGTP.LSELLR...E.QGLLSVKQGCCV.......GE....CGACTVLVD....................G..TAID.........................SCLYLAA
+YAGT_ECOLI/65-124                LKVNGK..TEQL.EVDTRTTLLDTLR...ENLHLIGTKKGCDH.......GQ....CGACTVLVN.....................GR......R....................LNACLTLAV
+DCMS_HYDPS/8-67                  VNVNGK..AQEK.AVEPRTLLIHFLR...EELNLTGAHIGCET.......SH....CGACTVDID.....................GR......S....................VKSCTHLAV
+Q52589_9PSED/8-67                MTVNGR..KVEE.AVEARTLLVHFLR...EKLNLTGTHIGCDT.......SH....CGACTVDVD.....................GK......S....................IKSCTHLAV
+O52837_BRAJA/6-65                LIVNGN..PVTA.NVDPRTLLVQFLR...ENLRLTGTHVGCDT.......SQ....CGACVVHLD.....................GK......A....................VKSCTTLAV
+O53709_MYCTU/5-64                MTVNGE..PVTA.EVEPRMLLVHFLR...DQLRLTGTHWGCDT.......SN....CGTCVVEVD.....................GV......P....................VKSCTMLAV
+O87682_ARTNI/8-67                VEVNGV..THAT.DVEPRRLLADFLR...DDLHLRGTRVGCEH.......GV....CGSCTVLLD.....................GQ......P....................VRSCTVLAV
+Q59128_ARTNI/14-73               VEVNGR..RRTV.AVDARETLADHLR...NDQKLTGIKLGCEH.......GV....CGACTILMD.....................GA......A....................VRSCLTLAA
+P72223_PSEPU/14-73               ATINGK..PRVF.YVEPRMHLADALR...EVVGLTGTKIGCEQ.......GV....CGSCTILID.....................GA......P....................MRSCLTLAV
+#=GR P72223_PSEPU/14-73    SS    EEE---..EEEE.EE-TTSBHHHHHH...HT------------.......--....----EEEE-.....................--......E....................EEGGGSBGG
+Q9ZBN8_STRCO/5-65                LTVNGR..PQEADDVWEGESLLYVLR...ERMGLPGSKNACEQ.......GE....CGSCTVRLD.....................GVP..........................VCSCLVAAG
+O54050_RHOCA/5-68                FLLNGE..TRRVRIEDPTQSLLELLR...A.EGLTGTKEGCNE.......GD....CGACTVMIRD.................AAGSR......A....................VNACLMMLP
+#=GR O54050_RHOCA/5-68     SS    EEE---..EEEEE-S-TT-BHHHHHH...H.------------.......--....----EEEEES.................----E......E....................EETTTSBGG
+O23887_MAIZE/15-85               LAVNGK..RYEAAGVAPSTSLLEFLR...TQTPVRGPKLGCGE.......GG....CGACVVLVSK.................YDPATDEVTEFS....................ASSCLTLLH
+ALDO4_ARATH/8-78                 FAVNGE..KFEVLSVNPSTTLLEFLR...SNTCFKSVKLSCGE.......GG....CGACIVILSK.................YDPVLDQVEEYS....................INSCLTLLC
+ALDO1_ARATH/23-95                FAINGQRFELELSSIDPSTTLVDFLR...NKTPFKSVKLGCGE.......GG....CGACVVLLSK.................YDPLLEKVDEFT....................ISSCLTLLC
+O30328_ACEEU/4-63                FRLNGR..EVTV.DVPGDTPLLWVIR...DEVGLTGTKFGCGI.......GM....CGACTIHIG.....................GR......A....................TRSCVTPVS
+IORA_BREDI/4-64                  FILNGQ..PVRVTEVPEDAPLLWVVR...EHLKLSGTKFGCGL.......GL....CGACTVHIN.....................GE......A....................ARSCITPLS
+XDH_EMENI/39-108                 FYLNGT..KVILDSVDPEITLLEYLR...G.IGLTGTKLGCAE.......GG....CGACTVVVS..........QIN.....PTTKKL....YHA..................SINACIAPLV
+O61198_CAEEL/8-78                FNVNGK..DIKEENVDPELTLAYYLR...NKLGLRGTKLGCEE.......GV....CGSCTVVLGT.................WDDSLNKAVYSA....................VNACLVPLF
+O17892_CAEEL/18-86               FYVNGK..RVEEKDVDPKMTLATYLR...DKLKLTGTKIGCNE.......GG....CGACTIMISH.................IENGE..IKHFS....................ANSCLMPVC
+XDH_DROSU/13-83                  FFVNGK..KVTDTNPDPECTLLTYLR...DKLRLCGTKLGCAE.......GG....CGACTVMISR.................MDRGQHKIRHLA....................VNACLTPVC
+O17506_BOMMO/19-89               FYVNGK..KVIESSPDPEWTLLWYLR...KKLRLTGTKLGCAE.......GG....CGACTVMVSK.................YNRQENKIIHLA....................VNACLAPVC
+Q17250_BOMMO/18-88               FFVNGK..KVLESNPDPEWTLLFYLR...KKLKLTGTKYGCGE.......GG....CGACTVMVSK.................YLKNEDRINHIA....................VNACLISVC
+ADO_BOVIN/9-79                   FYVNGR..KVTEKNVDPETMLLPYLR...KKLRLTGTKYGCGG.......GG....CGACTVMISR.................YNPITKKIRHYP....................ANACLTPIC
+XDH_BOVIN/8-78                   FFVNGK..KVVEKNADPETTLLAYLR...RKLGLRGTKLGCGE.......GG....CGACTVM............LSK.....YDRLQDKIIHFS....................ANACLAPIC
+#=GR XDH_BOVIN/8-78        SS    EEE---..EEEETT--TT-BHHHHHH...HT------------.......--....----EEE............EEE.....EETTTTEEEEEE....................EETTT-BGG
+MOP_DESGI/6-65                   ITVNGI..EQNL.FVDAEALLSDVLR...QQLGLTGVKVGCEQ.......GQ....CGACSVILD.....................GK......V....................VRACVTKMK
+#=GR MOP_DESGI/6-65        SS    EEE---..EEEE.EE-TTSBHHHHHH...HT------------.......--....----EEEE-.....................--......E....................EEGGG-BGG
+O53669_MYCTU/13-78               DESCGELREFTVEVNEGEVVLDVILRLQQTQTPDLAVRWNCKA.......GK....CGSCSAEIN.....................GKPR..........................LMCMTRMS
+O29566_ARCFU/5-80                TFL.PS..GKRAEVDEGKTILSAAQE...I.GEGIRS..LCGG.......KG...SCGKCL..VVVR........KGDVEILSEEAHEKFVRE..K.................GYYLACQTAVK
+O30225_ARCFU/5-84                TFE.PV..GKKVE.DEPDTILEIARR...N.GVLIRS..DCGG.......KG...VCGKCK..VVVVDY......RGSLSDITDHERKHLIEEEISK................GYRLACQARVE
+NQRF_CHLTR/46-122                NND.DS..LTKTV.DSGKTLLSSLLD...S.GIAIPS..PCGG.......KA...ACKQCK..VRIT.........KNADEPLETDRSTFSKQQLEQ................GWRLSCQTKVQ
+NQRF_HAEIN/43-119                NDD.PE..KAITL.PAGGKLLGALAS...K.GIFVSS..ACGG.......GG...SCGQCI..VKVK.........NGGGEILPTELSHINKREAKE................GYRLACQVNVK
+NQRF_VIBAL/39-115                NDD.PS..LAIVT.QPGGKLLSALAG...A.GVFVSS..ACGG.......GG...SCGQCR..VKVK.........SGGGDILPTELDHITKGEARE................GERLACQVAMK
+O84062_CHLTR/8-83                ADD......ENQEFHLEDGSSIAEV......CEHSGVPLACT........EG...VCGTCVIEVLEGA........DNLSDFSEAEYDFLGDPEDS.................NERLACQCCIK
+Q9Z8H9_CHLPN/8-83                SDD......EQQEFELEDNSEIAEP......CESMGIPFACT........EG...VCGTCVIEVLEGR........ENLSEFTEPEYDFLGEPEDS.................NERLACQCRIK
+CSMJ_CHLTE/5-82                  IND......KPCNAKVGDLLLNTAK......LNKAHIGYICGG.......NG...ICQSCFVYVLEGA........ECLSEPGEDEKAFISDKLFAE................GGRLACRTTIV
+CSMI_CHLTE/5-82                  IND......KTASSSVGQTIGKAAR......LNHAHVGYVCGG.......HG...LCQACYITVQEGA........DCLAPLTDVEKAFLSPRQIAA................GGRIACQATIA
+FER_TRIVA/13-90                  AVKGGVKKQLKFEDDQTLFTVLTEAG.......LMSADDTCQG.......NK...ACGKCICKHVSGKV......A.A..E..DDEKEFLEDQPAN..................ARLACAITLS
+#=GR FER_TRIVA/13-90       SS    EE----EEEE---TTEEHHHHHHT--.......----TTS---.......--...-----EEEEEE---......-.-..-..HHHHHHCTTS-TT..................EEEGGG-EE-
+P73774_SYNY3/7-88                LICLPD..NRLLEIDSNETILDALLK..G....DIAHISVCGG.......KA...NCSTCRIMVLDGIK.....NCSPPTSIEQALAKKLDFPFHV..................R.LACQTKLS
+FER_BUCAP/10-92                  KLLLPK..GGCFECKEGETILNVALK...N.NIKLEHA..CEK.......SC...ACSTCH..CIIRKG......FLSLSGWSEKEEDVLDKAWGLE...............STSRLSCQAIIG
+O69222_AZOVI/11-93               EVHCPE..GRVVEAETGESILEAALR...N.DIEIEHA..CEM.......SC...ACTTCH..VIVRDG......FDSLEPSDELEDDMLDKAWGLE...............PESRLSCQARVG
+FER_HAEIN/10-92                  EDFCPE..GMVVDAATGDN.LLEVAH...N.A.GVEIHHACDG.......SC...ACTTCHVIVREG........FDSLNETSDQEEDMLDKAWGLE...............MDSRLSCQCVVG
+FER_PSEAE/10-92                  ADHCPE..GAVFEAKPGET.ILDAAL...R.N.GIEIEHACEK.......SC...ACTTCHVIVREG........LDSMEPSDELEDDMLDKAWGLE...............PDSRLSCQAVVA
+ADRX_YEAST/67-149                LKD.GS..QKTYEVCEGETILDIAQG...H.NLDMEG..ACGG.......SC...ACSTCH.VIVDPDY......YDALPEPEDDENDMLDLAYGLT...............ETSRLGCQIKMS
+ADX_PIG/71-155                   NRD.GK..TLTTQGKVGDSLLDVVIE...N.NLDIDGFGACEG.......TL...ACSTCH.LIFEDHI......FEKLEAITDEENDMLDLAYGLT...............DRSRLGCQICLT
+FER2_RICPR/11-93                 IND.EE..ERTVEAPIGLSILEIAHS...N.DLDLEG..ACEG.......SL...ACATCH.VMLEEEF......YNKLKKPTEAEEDMLDLAFGLT...............DTSRLGCQIILT
+O49551_ARATH/44-127              DKD.GE..EIHIKVPVGMNILEAAHE...N.DIELEG..ACEG.......SL...ACSTCHVIVMDTKY......YNKLEEPTDEENDMLDLAFGLT...............ATSRLGCQVIAK
+ETP1_SCHPO/525-592               TPE.GR..EIMIE....GN......E...E.G.......ACEG.......SV...ACSTCHVIVDPEHY.....ELLD..PPEEDEEDMLDLAFGLE...............ETSRLGCQVLLR
+#=GR ETP1_SCHPO/525-592    SS    ---.--..EEEE-....--......-...-.-.......----.......--...--STT-EEE-HHHH.....HHS-..---HHHHHHHCTB----...............TTEE-----B--
+O07876_SPHSX/8-91                AAD.GR..EIETNVDIGTDLMHAGLY...N.SVPGLLG.ECSG.......GL...ACATCR.VHVPAEW......QGVLPAALPAEAELLGFCEESP...............PEARLSCQIKMT
+Q9ZAM5_SPHSX/8-91                SED.GS..ELETTVDVGVDLMHAGLY...N.SIPGILG.ECSG.......GL...ACATCR.VRVPVEW......QSILPPAFPSEAELLGFCDEAP...............PEARLSCQIKMT
+FER2_CAUCR/8-91                  QHD.GA..EQVIDVKPGLTVMEGAVK...N.NVPGIDA.DCGG.......AC...ACATCH.VYVDEAW......LDKTGDKSAMEESMLDFAENVE...............PNSRLSCQIKVS
+FER6_RHOCA/7-91                  EHN.GT..RHEVEAKPGLTVMEAARD...N.GVPGIDA.DCGG.......AC...ACSTCH.AYVDPAW......VDKLPKALPTETDMIDFAYEPNP..............ATSRLTCQIKVT
+#=GR FER6_RHOCA/7-91       SS    ---.--..EEEEE-----BHHHHHHT...-.-------.----.......--...SS-TTE.EEE-HHH......HTTS----HHHHHHHTTSSS--T..............TTEEEGGG-B--
+P74447_SYNY3/31-113              IKLDPIDLKVAIETNDNLLSGLLGQD........LRIMKECGG.......RG...MCATCHVYITAGMES...LSPLNRREQRTLEVITTHNRYS...................R.LACQARVL
+P73171_SYNY3/7-85                SFPQTKFLPLSLEFNACLAEYLTPDN........SPILFGCRT.......GL....CGTCLVKVVGEIL......SPEAEEREILAILAPDDVQA...................R.LACQIKLT
+FER1_AQUAE/3-83                  VIINGK....EFDIPKGVRFGELSHE.....IEKAGIEFGCTD.......GQ....CGVCVARVIKGMECL..NEPSEEEEETLWRVGAVDEDQR.....................LTCQLVIE
+FER4_RHOCA/7-86                  TFTDVS...ITVNVPTGTRIIEMSEK......VGSGITYGCRE.......GE....CGTCMTHILEGSE.....NLSEPTALEMRVLEENLGGKD...................DRLACQCRVL
+P74283_SYNY3/5-88                FVKEQK....DIVVAQGANLREKALQNGVDIYTLKGKLMNCGG......YGQ....CGTCIVEITAGME.....NLSPKTDFENRVLRKKPDNFR.....................LACQTLVN
+PUTX_PSEPU/8-92                  SHD.GT..RRELDVADGVS.LMQAAV...S.NGIYDIVGDCGG.......SA...SCATCHVYVN................EAFTDKVP.....AANEREIGMLECVTAELKPNSRLCCQIIMT
+#=GR PUTX_PSEPU/8-92       SS    E--.--..EEEEE-----B.HHHHHH...H.---TTG------.......--...SSSTTEEEE-................TTTGTTS-.....---TTT---GGGSSS---TTEEEGGG-B--
+TERPB_PSESP/8-92                 DEQSGE...YAVDAQDGQS.LMEVAT...Q.NGVPGIVAECGG.......SC...VCATCRIEIEDAWV......E.......IVGEANPDENDLLQSTGE........PMTAGTRLSCQVFID
+P95277_MYCTU/9-84                GYSDGT..HKTMPVRCDQT.VLDAAE.....EHGVAIVNECQS.......GI....CGTCVATCTAGRYQ....MG.R...TEGLSDVERAARKI.....................LTCQTFVT
+O05933_PSEPU/11-88               NFSDGV..SRSFDVEAGTS.ILDAAI.....ESEIPLLYQCRS.......GS....CSTCIAQLTEGEAH....TRAG..ASSTLLASEYASGQR.....................LLCLCQAQ
+DESET_MYCTU/303-373              FARSGK....SVAADAATS.LMDAGE.....GAGVQLPFGCRM.......GI....CQSCVVDLVEGHV......R.D.....LRTGQRHEPGTR....................VQTCVSAAS
+O23344_ARATH/57-131              VEHDGK..TTELEVEPDETILSKALD...S...GLDVPYDCNL.......GV....CMTCPAKLVTGTV.....DQSG....GMLSDDVVERGYT.....................LLCASYPT
+P74159_SYNY3/11-86               DRQNEK..DYSVIVSDDRYILHQAED...Q...GFELPFSCRN.......GA....CTACAVRVISGQIH....QP....EAMGLSPDLQRQGYA.....................LLCVSYAQ
+FER2_SYNP6/8-83                  VIYQGQ..SQTFTADSDQS.VLDSAQ...A.A.GVDLPASCLT.......GV....CTTCAARILSGEV.....DQPD...AMGVGPEPAKQGYT.....................LLCVAYPR
+P73388_SYNY3/9-84                IQHQGQ..TYTISVPEDKT.VLQAAD...D.E.GIQLPTSCGA.......GV....CTTCAALITEGTA.....EQAD...GMGVSAELQAEGYA.....................LLCVAYPR
+FER1_HALMA/35-108                DEDYGS.....LEVNEGEY.ILEAAE...A.Q.GYDWPFSCRA.......GA....CANCAAIVLEGDI.....DM..D.MQQILSDEEVEDKNV....................RLTCIGSPD
+P74449_SYNY3/11-88               NPATGS..DVTIEVAEDEL.ILEAAE...N.Q.GLDLPYSCRA.......AS....CVACAGRLLEGTVE...HTDKG...SDFLKPEELAAGCV.....................LLCAAYAT
+FER2_NOSMU/10-85                 NAAEGL..DETIEVPDDEY.ILDAAE...E.A.GLDLPFSCRS.......GS....CSSCNGILKKGTV.....DQSD...QNFLDDDQIAAGNV.....................LTCVAYPT
+FER2_APHSA/10-86                 NEEEGI..NAILEVADDQT.ILDAGE...E.A.GLDLPSSCRA.......GS....CSTCAGKLVSGAA.......PNQDDQAFLDDDQLAAGWV.....................MTCVAYPT
+FER1_CYAPA/10-85                 CEEQGL..DTTIECPDDEY.ILDAAE...E.Q.GIDLPYSCRA.......GA....CSTCAGKVVEGTV.....DQSD...QSFLDDAQLAAGYV.....................LTCVAYPS
+FER_PORPU/10-85                  SEDEGI..DVTFDCSEDTY.ILDAAE...E.A.GIELPYSCRA.......GA....CSTCAGKVTEGSV.....DQSD...QSFLDDEQLLKGYV.....................LTCIAYPE
+FER_ODOSI/10-85                  SEEHDI..DATIDCNDDVF.LLDAAE...E.Q.GIELPYSCRA.......GA....CSTCAGKVTEGDI.....DQSE...QTFLDDDQVGAGFV.....................LTCIAYPK
+FER_BUMFI/9-84                   NEEKNI..NAVIKCPDDQF.ILDAAE...E.Q.GIELPYSCRA.......GA....CSTCAGKVLSGTI.....DQSE...QSFLDDDQMGAGFL.....................LTCVAYPT
+FER3_CYACA/9-84                  NKDQGI..DETIECPDDQY.ILDAAE...E.Q.GLDLPYSCRA.......GA....CSTCAGKLLEGEV.....DQSD...QSFLDDDQVKAGFV.....................LTCVAYPT
+FER2_CYACA/8-83                  NQKEGV..DVTINCPGDQY.ILDAAE...E.Q.GVDLPYSCRA.......GA....CSTCAGKLVKGSV.....DQSD...QSFLDEEQINNGFI.....................LTCVAYPT
+FER_BRYMA/8-83                   KLDDGS..EAVIDCDEDSF.ILDVAE...E.E.GIDIPFSCRS.......GS....CSTCAGKIEGGTV.....DQSE...QTFLDDDQMEEGYV.....................LTCVAYPT
+FER_APHSA/9-83                   KTPDGD..NVIT.VPDDEY.ILDVAE...E.E.GLDLPYSCRA.......GA....CSTCAGKLVSG........PAPDEDQSFLDDDQIQAGYI.....................LTCVAYPT
+FER_THEVL/9-84                   VRPDGS..ETTIDVPEDEY.ILDVAE...E.Q.GLDLPFSCRA.......GA....CSTCAGKLLEGEV.....DQSD...QSFLDDDQIEKGFV.....................LTCVAYPR
+FER_PERBI/6-80                   DTPDGK...KSFECPGDSY.ILDKAE...E.E.GLELPYSCRA.......GS....CSSCAGKVLTGSI.....DQSD...QAFLDDDQGGDGYC.....................LTCVTYPT
+FER3_RAPSA/8-82                  ITPEGE...QEVECDDDVY.VLDAAE...E.A.GIDLPYSCRA.......GS....CSSCAGKVVSGSV.....DQSD...QSFLDDDQIAEGFV.....................LTCAAYPT
+FER1_SPIOL/58-132                VTPTGN...VEFQCPDDVY.ILDAAE...E.E.GIDLPYSCRA.......GS....CSSCAGKLKTGSL.....NQDD...QSFLDDDQIDEGWV.....................LTCAAYPV
+FER_SILPR/57-131                 TKESGT...VTFDCPDDVY.VLDQAE...E.E.GIDLPYSCRA.......GS....CSSCAGKVVAGSV.....DQSD...QSFLDDDQIEAGWV.....................LTCAAYPS
+FER_WHEAT/54-128                 VTPEGE...VELEVPDDVY.ILDQAE...E.E.GIDLPYSCRA.......GS....CSSCAGKLVSGEI.....DQSD...QSFLDDDQMEAGWV.....................LTCHAYPK
+FER_SAMNI/8-82                   ITPDGP...QEFECPDDVY.ILEHAE...E.L.GIDIPYSCRA.......GS....CSSCAGKLVAGSV.....DQSD...QSFLDDEQIEEGWV.....................LTCVAYPK
+FERA_ALOMA/8-82                  VTPQGQ...QEFDCPDDVY.ILDQAE...E.E.GIDLPYSCRA.......GS....CSSCAGKVKQGEV.....DQSD...GSFLDDEQMEQGWV.....................LTCVAFPT
+FER_ARCLA/8-82                   ITPEGK...QEFEVPDDVY.ILDHAA...E.E.VGDLPYSCRA.......GS....CSSCAGKVTAGSV.....DQSD...GSYLDDDQMEAGWV.....................LTCVAYPT
+FER_DATST/8-82                   VTPDGP...VEFNCPDDVY.ILDQAE...E.E.GHDLPYSCRA.......GS....CSSCAGKVTAGTV.....DQSD...GNYLDDDQMADGFV.....................LTCVAYPQ
+FER_PALPL/9-83                   STPGGV...EEIEGDETTY.VLDSAE...D.Q.GIDLPYSCRA.......GA....CSTCAGIVELGTV.....DQSD...QSFLDDDQLNDSFV.....................LTCVAYPT
+FER_EUGVI/8-82                   INPDGE..VTI.ECGEDQY.ILDAAE...D.A.GIDLPYSCRA.......GA....CSSCTGIVKEGTV.....DQSD...QSFLDDDQMAKGFC.....................LTCTTYPT
+FER_CHLFU/6-80                   KTPSGE...ETIECPEDTY.ILDAAE...E.A.GLDLPYSCRA.......GA....CSSCAGKVESGEV.....DQSD...QSFLDDAQMGKGFV.....................LTCVAYPT
+FER_SYNY4/9-83                   ITPDGE...NSIECSDDTY.ILDAAE...E.A.GLDLPYSCRA.......GA....CSTCAGKITAGSV.....DQSD...QSFLDDDQIEAGYV.....................LTCVAYPT
+FER1_PHYAM/8-82                  VTPSGT...QTIDCPDDTY.VLDAAE...E.A.GLDLPYSCRA.......GS....CSSCTGKVTAGTV.....DQED...QSFLDDDQIEAGFV.....................LTCVAFPK
+FER2_PHYAM/9-83                  VTPSGT...NTITCPADTY.VLDAAE...E.S.GLDLPYSCRA.......GA....CSSCAGKVTAGAV.....NQED...GSFLEEEQMEAGWV.....................LTCVAYPT
+FER2_SPIOL/8-82                  VTPSGS...QVIECGDDEY.ILDAAE...E.K.GMDLPYSCRA.......GA....CSSCAGKVTSGSV.....DQSD...QSFLEDGQMEEGWV.....................LTCIAYPT
+FER_PHYPA/57-132                 DGETGA..ENVXECSDEEY.XLDAAE...R.A.GMDLPYSCRA.......GA....CSSCAGIIKAGEV.....DQSD...QSFLDDSQIDDGFV.....................LTCVAYPA
+FER_MARPO/7-81                   NTPTGQ...SVIDVEDDEY.ILDAAE...E.A.GLSLPYSCRA.......GA....CSSCAGKVTAGEV.....DQSD...ESFLDDDQMDEGYV.....................LTCIAYPT
+#=GC SS_cons                     EEESS-EEEEEEEEEETTCBHHHHHH...HTT-TTTGTTSS--TT..S..--...SSSTTEEEEEEHCEE....EHCCS..TTHHHHHHHTTSSET-TTT---GGGSSS---TTEEECCCSBGG
+#=GC seq_cons                    hphsup..thphpsssspp.lLcshc...p.t.slslshuCps.......Gs....CusCtsplhtu.................hpspphttt.h.....................LuCtshsp
+//

diff --git a/examples/testdata/example_annot_file.jva b/examples/testdata/example_annot_file.jva
new file mode 100644 (file)
index 0000000..794f42b
--- /dev/null
+++ b/examples/testdata/example_annot_file.jva
@@ -0,0 +1,22 @@
+#Comment lines follow the hash symbol
+JALVIEW_ANNOTATION
+SEQUENCE_REF   FER1_MESCR      5
+BAR_GRAPH      Bar Graph 1     <html>an <em>html tooltip</em> for Bar graph 1.</html>  ||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
+LINE_GRAPH     Green Values    1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2
+LINE_GRAPH     Red Values      2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2
+BAR_GRAPH      Bar Graph       2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
+NO_GRAPH       Icons   ||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
+NO_GRAPH       Purple Letters  m|y|p|r|o|t|e|i|n
+COLOUR Bar Graph 2     blue
+COLOUR Red Values      255,0,0
+COLOUR Green Values    green
+COLOUR Purple Letters  151,52,228
+COMBINE        Green Values    Red Values
+GRAPHLINE      Red Values      2.6     threshold       black
+
+SEQUENCE_GROUP Group_A 30      50      *
+SEQUENCE_GROUP Group_B 1       351     2-5
+SEQUENCE_GROUP Group_C 12      14      -1      seq1    seq2    seq3
+PROPERTIES     Group_A description=This is the description     colour=Helix Propensity pidThreshold=0  outlineColour=red       displayBoxes=true       displayText=false       colourText=false        textCol1=black  textCol2=black  textColThreshold=0
+PROPERTIES     Group_B outlineColour=red
+PROPERTIES     Group_C colour=Clustal

diff --git a/examples/testdata/test_combine_annot.jva b/examples/testdata/test_combine_annot.jva
new file mode 100644 (file)
index 0000000..e1ee9e0
--- /dev/null
+++ b/examples/testdata/test_combine_annot.jva
@@ -0,0 +1,31 @@
+#Comment lines follow the hash symbol
+JALVIEW_ANNOTATION
+SEQUENCE_REF   FER1_MESCR      5
+BAR_GRAPH      Bar Graph 1     <html>an <em>html tooltip</em> for Bar graph 1.</html>  ||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
+LINE_GRAPH     Green Values    1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2
+LINE_GRAPH     Red Values      2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2
+LINE_GRAPH     Blue Values     0|0|0|1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2
+LINE_GRAPH     Yellow Values   3.0|3.0|3.0|2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2
+
+BAR_GRAPH      Bar Graph       2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
+
+NO_GRAPH       Icons   ||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
+NO_GRAPH       Purple Letters  m|y|p|r|o|t|e|i|n
+COLOUR Bar Graph 2     blue
+COLOUR Red Values      255,0,0
+COLOUR Green Values    green
+COLOUR Blue Values     blue
+COLOUR Yellow Values   yellow
+COLOUR Purple Letters  151,52,228
+
+COMBINE        Green Values    Red Values
+COMBINE        Blue Values     Yellow Values
+
+GRAPHLINE      Red Values      2.6     threshold       black
+
+SEQUENCE_GROUP Group_A 30      50      *
+SEQUENCE_GROUP Group_B 1       351     2-5
+SEQUENCE_GROUP Group_C 12      14      -1      seq1    seq2    seq3
+PROPERTIES     Group_A description=This is the description     colour=Helix Propensity pidThreshold=0  outlineColour=red       displayBoxes=true       displayText=false       colourText=false        textCol1=black  textCol2=black  textColThreshold=0
+PROPERTIES     Group_B outlineColour=red
+PROPERTIES     Group_C colour=Clustal

diff --git a/examples/testdata/uniref50_iupred.jva b/examples/testdata/uniref50_iupred.jva
new file mode 100644 (file)
index 0000000..dcc5601
--- /dev/null
+++ b/examples/testdata/uniref50_iupred.jva
@@ -0,0 +1,172 @@
+JALVIEW_ANNOTATION
+# Created: Thu May 23 15:10:57 BST 2013
+
+BAR_GRAPH      Conservation    Conservation of total alignment less than 25% gaps      1.0,1,1.0,[5d1500]|3.0,3,3.0,[7d3f00]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|1.0,1,1.0,[5d1500]|2.0,2,2.0,[6d2a00]|0.0,0,0.0,[4d0000]|1.0,1,1.0,[5d1500]|0.0,0,0.0,[4d0000]|1.0,1,1.0,[5d1500]|0.0,0,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,0,0.0,[4d0000]|1.0,1,1.0,[5d1500]|0.0,0,0.0,[4d0000]|0.0,0,0.0,[4d0000]|0.0,0,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,0,0.0,[4d0000]|0.0,0,0.0,[4d0000]|0.0,0,0.0,[4d0000]|0.0,0,0.0,[4d0000]|0.0,0,0.0,[4d0000]|0.0,0,0.0,[4d0000]|0.0,0,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|2.0,2,2.0,[6d2a00]|1.0,1,1.0,[5d1500]|1.0,1,1.0,[5d1500]|1.0,1,1.0,[5d1500]|0.0,0,0.0,[4d0000]|0.0,0,0.0,[4d0000]|1.0,1,1.0,[5d1500]|0.0,-,0.0,[4d0000]|2.0,2,2.0,[6d2a00]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,0,0.0,[4d0000]|0.0,0,0.0,[4d0000]|0.0,0,0.0,[4d0000]|1.0,1,1.0,[5d1500]|0.0,0,0.0,[4d0000]|11.0,*,11.0,[ffe600]|7.0,7,7.0,[be9200]|11.0,*,11.0,[ffe600]|6.0,6,6.0,[ae7d00]|11.0,*,11.0,[ffe600]|6.0,6,6.0,[ae7d00]|8.0,8,8.0,[cea700]|9.0,9,9.0,[dfbc00]|11.0,*,11.0,[ffe600]|11.0,*,11.0,[ffe600]|7.0,7,7.0,[be9200]|11.0,*,11.0,[ffe600]|3.0,3,3.0,[7d3f00]|6.0,6,6.0,[ae7d00]|11.0,*,11.0,[ffe600]|7.0,7,7.0,[be9200]|7.0,7,7.0,[be9200]|9.0,9,9.0,[dfbc00]|5.0,5,5.0,[9e6800]|6.0,6,6.0,[ae7d00]|8.0,8,8.0,[cea700]|11.0,*,11.0,[ffe600]|11.0,*,11.0,[ffe600]|9.0,9,9.0,[dfbc00]|11.0,*,11.0,[ffe600]|11.0,*,11.0,[ffe600]|3.0,3,3.0,[7d3f00]|11.0,*,11.0,[ffe600]|11.0,*,11.0,[ffe600]|11.0,*,11.0,[ffe600]|3.0,3,3.0,[7d3f00]|11.0,*,11.0,[ffe600]|5.0,5,5.0,[9e6800]|9.0,9,9.0,[dfbc00]|11.0,*,11.0,[ffe600]|11.0,*,11.0,[ffe600]|9.0,9,9.0,[dfbc00]|11.0,*,11.0,[ffe600]|11.0,*,11.0,[ffe600]|11.0,*,11.0,[ffe600]|11.0,*,11.0,[ffe600]|11.0,*,11.0,[ffe600]|11.0,*,11.0,[ffe600]|11.0,*,11.0,[ffe600]|11.0,*,11.0,[ffe600]|11.0,*,11.0,[ffe600]|11.0,*,11.0,[ffe600]|11.0,*,11.0,[ffe600]|11.0,*,11.0,[ffe600]|11.0,*,11.0,[ffe600]|9.0,9,9.0,[dfbc00]|3.0,3,3.0,[7d3f00]|7.0,7,7.0,[be9200]|11.0,*,11.0,[ffe600]|3.0,3,3.0,[7d3f00]|9.0,9,9.0,[dfbc00]|8.0,8,8.0,[cea700]|11.0,*,11.0,[ffe600]|6.0,6,6.0,[ae7d00]|11.0,*,11.0,[ffe600]|4.0,4,4.0,[8d5300]|5.0,5,5.0,[9e6800]|9.0,9,9.0,[dfbc00]|11.0,*,11.0,[ffe600]|8.0,8,8.0,[cea700]|9.0,9,9.0,[dfbc00]|0.0,0,0.0,[4d0000]|1.0,1,1.0,[5d1500]|0.0,0,0.0,[4d0000]|0.0,0,0.0,[4d0000]|0.0,0,0.0,[4d0000]|3.0,3,3.0,[7d3f00]|2.0,2,2.0,[6d2a00]|3.0,3,3.0,[7d3f00]|2.0,2,2.0,[6d2a00]|2.0,2,2.0,[6d2a00]|2.0,2,2.0,[6d2a00]|1.0,1,1.0,[5d1500]|3.0,3,3.0,[7d3f00]|2.0,2,2.0,[6d2a00]|2.0,2,2.0,[6d2a00]|0.0,0,0.0,[4d0000]|1.0,1,1.0,[5d1500]|4.0,4,4.0,[8d5300]|3.0,3,3.0,[7d3f00]|1.0,1,1.0,[5d1500]|2.0,2,2.0,[6d2a00]|3.0,3,3.0,[7d3f00]|2.0,2,2.0,[6d2a00]|5.0,5,5.0,[9e6800]|3.0,3,3.0,[7d3f00]|3.0,3,3.0,[7d3f00]|0.0,0,0.0,[4d0000]|0.0,0,0.0,[4d0000]|1.0,1,1.0,[5d1500]|0.0,0,0.0,[4d0000]|0.0,-,0.0,[4d0000]|0.0,-,0.0,[4d0000]|
+BAR_GRAPH      Quality Alignment Quality based on Blosum62 scores      29.151815,29.151815,[cba200]|30.574812,30.574812,[d1aa00]|14.400199,14.400199,[8b5000]|16.93248,16.93248,[965e00]|2.1220763,2.1220763,[560c00]|2.2049963,2.2049963,[560c00]|3.647952,3.647952,[5c1400]|4.814642,4.814642,[611b00]|18.351393,18.351393,[9c6600]|17.532412,17.532412,[996200]|7.5054855,7.5054855,[6d2a00]|15.490477,15.490477,[905600]|14.241707,14.241707,[8a4f00]|9.905579,9.905579,[773700]|20.354017,20.354017,[a57100]|26.870352,26.870352,[c19600]|24.969187,24.969187,[b98b00]|27.419409,27.419409,[c39900]|15.350427,15.350427,[8f5600]|21.116522,21.116522,[a87600]|9.34032,9.34032,[753400]|14.1895275,14.1895275,[8a4f00]|10.104505,10.104505,[783800]|8.587312,8.587312,[723000]|18.694708,18.694708,[9e6800]|11.420612,11.420612,[7e4000]|6.8467255,6.8467255,[6a2600]|17.449827,17.449827,[986100]|16.825909,16.825909,[955e00]|2.4334474,2.4334474,[570e00]|15.685622,15.685622,[915700]|9.836516,9.836516,[773700]|3.4712791,3.4712791,[5c1300]|4.531816,4.531816,[601900]|7.8744216,7.8744216,[6f2c00]|0.0,0.0,[4d0000]|9.01113,9.01113,[743200]|3.174218,3.174218,[5a1200]|2.0395048,2.0395048,[550b00]|2.1654668,2.1654668,[560c00]|21.517344,21.517344,[aa7800]|15.738462,15.738462,[915800]|14.844854,14.844854,[8d5300]|22.159096,22.159096,[ad7c00]|13.956608,13.956608,[894e00]|20.147892,20.147892,[a47000]|25.067545,25.067545,[b98c00]|2.0943506,2.0943506,[560c00]|20.30842,20.30842,[a57100]|10.254437,10.254437,[793900]|6.5836596,6.5836596,[692500]|19.446732,19.446732,[a16c00]|6.2202287,6.2202287,[672300]|9.796006,9.796006,[773700]|6.0385494,6.0385494,[672200]|13.963727,13.963727,[894e00]|13.838549,13.838549,[884d00]|18.48424,18.48424,[9d6700]|18.302633,18.302633,[9c6600]|41.172745,41.172745,[ffe600]|32.59908,32.59908,[dab600]|41.172745,41.172745,[ffe600]|34.495945,34.495945,[e2c000]|41.172745,41.172745,[ffe600]|33.501804,33.501804,[debb00]|27.034466,27.034466,[c29700]|40.020737,40.020737,[fadf00]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|29.252739,29.252739,[cba300]|41.172745,41.172745,[ffe600]|14.935498,14.935498,[8d5300]|0.88449144,0.88449144,[500500]|41.172745,41.172745,[ffe600]|20.81991,20.81991,[a77400]|31.73346,31.73346,[d6b100]|29.757969,29.757969,[cea600]|16.279755,16.279755,[935b00]|32.647984,32.647984,[dab600]|38.352337,38.352337,[f3d600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|39.6125,39.6125,[f8dd00]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|9.671661,9.671661,[763600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|11.17141,11.17141,[7d3e00]|41.172745,41.172745,[ffe600]|3.2054348,3.2054348,[5a1200]|38.569283,38.569283,[f4d700]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|39.707684,39.707684,[f9dd00]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|41.172745,41.172745,[ffe600]|39.447525,39.447525,[f8dc00]|21.229778,21.229778,[a97600]|27.779364,27.779364,[c59b00]|41.172745,41.172745,[ffe600]|24.149143,24.149143,[b58700]|39.447525,39.447525,[f8dc00]|33.857655,33.857655,[dfbd00]|41.172745,41.172745,[ffe600]|28.69976,28.69976,[c9a000]|41.172745,41.172745,[ffe600]|14.611241,14.611241,[8c5100]|32.346375,32.346375,[d9b400]|39.24055,39.24055,[f7db00]|41.172745,41.172745,[ffe600]|38.352337,38.352337,[f3d600]|38.569283,38.569283,[f4d700]|22.374107,22.374107,[ae7d00]|36.98438,36.98438,[edce00]|12.34415,12.34415,[824500]|11.811655,11.811655,[804200]|14.798897,14.798897,[8d5200]|36.60138,36.60138,[ebcc00]|14.0762415,14.0762415,[8a4e00]|36.817875,36.817875,[eccd00]|36.53897,36.53897,[ebcc00]|37.583706,37.583706,[efd100]|35.536423,35.536423,[e7c600]|18.004925,18.004925,[9b6400]|37.633095,37.633095,[f0d200]|34.738743,34.738743,[e3c200]|36.451622,36.451622,[ebcb00]|19.948801,19.948801,[a36f00]|28.285,28.285,[c79e00]|35.93151,35.93151,[e8c800]|36.817875,36.817875,[eccd00]|26.762383,26.762383,[c19500]|36.37101,36.37101,[eacb00]|36.413998,36.413998,[eacb00]|37.583706,37.583706,[efd100]|36.282784,36.282784,[eaca00]|34.729824,34.729824,[e3c200]|36.413998,36.413998,[eacb00]|24.348654,24.348654,[b68800]|24.349539,24.349539,[b68800]|34.091675,34.091675,[e0be00]|21.114677,21.114677,[a87600]|13.676696,13.676696,[884c00]|2.1107035,2.1107035,[560c00]|
+BAR_GRAPH      Consensus       PID     80.0,M,M 80%|80.0,A,A 80%|20.0,+,[AST] 20%|53.333332,T,T 53%|0.0,-,- 0%|0.0,-,- 0%|13.333333,T,T 13%|20.0,P,P 20%|40.0,A,A 40%|40.0,L,L 40%|46.666668,S,S 46%|40.0,G,G 40%|33.333332,T,T 33%|20.0,+,[AIM] 20%|33.333332,V,V 33%|66.666664,S,S 66%|66.666664,T,T 66%|66.666664,S,S 66%|66.666664,F,F 66%|46.666668,L,L 46%|46.666668,R,R 46%|46.666668,R,R 46%|26.666666,Q,Q 26%|46.666668,P,P 46%|40.0,A,A 40%|60.0,P,P 60%|26.666666,T,T 26%|53.333332,S,S 53%|40.0,L,L 40%|20.0,R,R 20%|26.666666,S,S 26%|33.333332,L,L 33%|40.0,P,P 40%|26.666666,S,S 26%|33.333332,+,[AN] 33%|26.666666,V,V 26%|33.333332,G,G 33%|20.0,+,[EQ] 20%|0.0,-,- 0%|0.0,-,- 0%|33.333332,+,[AS] 33%|53.333332,L,L 53%|60.0,F,F 60%|73.333336,G,G 73%|66.666664,L,L 66%|66.666664,K,K 66%|53.333332,S,S 53%|0.0,-,- 0%|40.0,S,S 40%|26.666666,T,T 26%|20.0,A,A 20%|66.666664,R,R 66%|40.0,G,G 40%|53.333332,G,G 53%|46.666668,R,R 46%|33.333332,V,V 33%|46.666668,T,T 46%|53.333332,A,A 53%|66.666664,M,M 66%|100.0,A,A 100%|53.333332,T,T 53%|100.0,Y,Y 100%|86.666664,K,K 86%|100.0,V,V 100%|86.666664,K,K 86%|66.666664,L,L 66%|80.0,I,I 80%|100.0,T,T 100%|100.0,P,P 100%|66.666664,E,E 66%|100.0,G,G 100%|46.666668,E,E 46%|46.666668,Q,Q 46%|100.0,E,E 100%|46.666668,F,F 46%|60.0,E,E 60%|86.666664,C,C 86%|66.666664,P,P 66%|80.0,D,D 80%|93.333336,D,D 93%|100.0,V,V 100%|100.0,Y,Y 100%|66.666664,I,I 66%|100.0,L,L 100%|100.0,D,D 100%|46.666668,A,A 46%|100.0,A,A 100%|100.0,E,E 100%|100.0,E,E 100%|53.333332,A,A 53%|100.0,G,G 100%|60.0,I,I 60%|93.333336,D,D 93%|100.0,L,L 100%|100.0,P,P 100%|93.333336,Y,Y 93%|100.0,S,S 100%|100.0,C,C 100%|100.0,R,R 100%|100.0,A,A 100%|100.0,G,G 100%|100.0,S,S 100%|100.0,C,C 100%|100.0,S,S 100%|100.0,S,S 100%|100.0,C,C 100%|100.0,A,A 100%|100.0,G,G 100%|100.0,K,K 100%|80.0,V,V 80%|60.0,V,V 60%|53.333332,S,S 53%|100.0,G,G 100%|60.0,S,S 60%|80.0,V,V 80%|80.0,D,D 80%|100.0,Q,Q 100%|66.666664,S,S 66%|100.0,D,D 100%|46.666668,+,[GQ] 46%|73.333336,S,S 73%|93.333336,F,F 93%|100.0,L,L 100%|93.333336,D,D 93%|93.333336,D,D 93%|53.333332,D,D 53%|93.333336,Q,Q 93%|53.333332,I,I 53%|40.0,A,A 40%|53.333332,E,E 53%|93.333336,G,G 93%|46.666668,W,W 46%|93.333336,V,V 93%|93.333336,L,L 93%|93.333336,T,T 93%|93.333336,C,C 93%|53.333332,V,V 53%|93.333336,A,A 93%|86.666664,Y,Y 86%|93.333336,P,P 93%|60.0,T,T 60%|73.333336,S,S 73%|93.333336,D,D 93%|93.333336,V,V 93%|66.666664,T,T 66%|93.333336,I,I 93%|93.333336,E,E 93%|93.333336,T,T 93%|93.333336,H,H 93%|86.666664,K,K 86%|93.333336,E,E 93%|73.333336,E,E 73%|60.0,E,E 60%|73.333336,L,L 73%|46.666668,T,T 46%|40.0,A,A 40%|0.0,-,- 0%|
+
+SEQUENCE_REF   FER2_ARATH
+LINE_GRAPH     IUPredWS (Long) <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.1671,0.1671,[72144e]|0.2129,0.2129,[72144e]|0.247,0.247,[72144e]|0.1554,0.1554,[72144e]|0.1162,0.1162,[72144e]|0.1449,0.1449,[72144e]|0.1731,0.1731,[72144e]|0.2064,0.2064,[72144e]|0.2436,0.2436,[72144e]|0.2715,0.2715,[72144e]|0.3249,0.3249,[72144e]|0.2783,0.2783,[72144e]|0.3019,0.3019,[72144e]|0.2399,0.2399,[72144e]|0.2364,0.2364,[72144e]|0.2645,0.2645,[72144e]|0.2609,0.2609,[72144e]|0.2988,0.2988,[72144e]|0.2064,0.2064,[72144e]|0.2094,0.2094,[72144e]|0.2849,0.2849,[72144e]|0.3426,0.3426,[72144e]|0.3529,0.3529,[72144e]|0.3426,0.3426,[72144e]|0.2817,0.2817,[72144e]|0.2783,0.2783,[72144e]|0.3426,0.3426,[72144e]|0.2715,0.2715,[72144e]|0.2609,0.2609,[72144e]|0.2503,0.2503,[72144e]|0.2364,0.2364,[72144e]|0.2364,0.2364,[72144e]|0.1791,0.1791,[72144e]|0.247,0.247,[72144e]|0.2503,0.2503,[72144e]|0.3149,0.3149,[72144e]|0.3149,0.3149,[72144e]|0.2645,0.2645,[72144e]|0.3356,0.3356,[72144e]|0.2752,0.2752,[72144e]|0.346,0.346,[72144e]|0.346,0.346,[72144e]|0.3426,0.3426,[72144e]|0.2645,0.2645,[72144e]|0.247,0.247,[72144e]|0.1969,0.1969,[72144e]|0.2503,0.2503,[72144e]|0.2503,0.2503,[72144e]|0.1852,0.1852,[72144e]|0.2541,0.2541,[72144e]|0.2951,0.2951,[72144e]|0.3182,0.3182,[72144e]|0.3215,0.3215,[72144e]|0.3392,0.3392,[72144e]|0.374,0.374,[72144e]|0.3948,0.3948,[72144e]|0.3392,0.3392,[72144e]|0.3599,0.3599,[72144e]|0.268,0.268,[72144e]|0.3426,0.3426,[72144e]|0.3599,0.3599,[72144e]|0.4051,0.4051,[72144e]|0.374,0.374,[72144e]|0.3249,0.3249,[72144e]|0.268,0.268,[72144e]|0.2783,0.2783,[72144e]|0.3019,0.3019,[72144e]|0.3286,0.3286,[72144e]|0.3117,0.3117,[72144e]|0.4292,0.4292,[72144e]|0.5296,0.5296,[72144e]|0.4901,0.4901,[72144e]|0.4582,0.4582,[72144e]|0.3667,0.3667,[72144e]|0.384,0.384,[72144e]|0.2918,0.2918,[72144e]|0.3182,0.3182,[72144e]|0.2193,0.2193,[72144e]|0.2752,0.2752,[72144e]|0.1643,0.1643,[72144e]|0.2541,0.2541,[72144e]|0.2034,0.2034,[72144e]|0.1852,0.1852,[72144e]|0.1702,0.1702,[72144e]|0.1399,0.1399,[72144e]|0.2034,0.2034,[72144e]|0.2541,0.2541,[72144e]|0.2292,0.2292,[72144e]|0.1881,0.1881,[72144e]|0.2129,0.2129,[72144e]|0.2292,0.2292,[72144e]|0.1643,0.1643,[72144e]|0.107,0.107,[72144e]|0.1251,0.1251,[72144e]|0.1251,0.1251,[72144e]|0.1759,0.1759,[72144e]|0.1115,0.1115,[72144e]|0.1731,0.1731,[72144e]|0.1501,0.1501,[72144e]|0.2164,0.2164,[72144e]|0.2328,0.2328,[72144e]|0.3286,0.3286,[72144e]|0.3286,0.3286,[72144e]|0.2645,0.2645,[72144e]|0.2034,0.2034,[72144e]|0.2193,0.2193,[72144e]|0.3286,0.3286,[72144e]|0.3529,0.3529,[72144e]|0.3631,0.3631,[72144e]|0.4292,0.4292,[72144e]|0.4541,0.4541,[72144e]|0.4766,0.4766,[72144e]|0.4864,0.4864,[72144e]|0.4652,0.4652,[72144e]|0.4685,0.4685,[72144e]|0.4051,0.4051,[72144e]|0.4087,0.4087,[72144e]|0.3117,0.3117,[72144e]|0.3321,0.3321,[72144e]|0.2918,0.2918,[72144e]|0.2164,0.2164,[72144e]|0.2503,0.2503,[72144e]|0.2364,0.2364,[72144e]|0.2292,0.2292,[72144e]|0.2503,0.2503,[72144e]|0.2918,0.2918,[72144e]|0.3053,0.3053,[72144e]|0.2258,0.2258,[72144e]|0.2292,0.2292,[72144e]|0.2129,0.2129,[72144e]|0.2064,0.2064,[72144e]|0.2164,0.2164,[72144e]|0.2436,0.2436,[72144e]|0.2436,0.2436,[72144e]|0.2193,0.2193,[72144e]|0.2258,0.2258,[72144e]|0.2503,0.2503,[72144e]|0.3117,0.3117,[72144e]|0.2884,0.2884,[72144e]|0.374,0.374,[72144e]|0.4149,0.4149,[72144e]|0.4292,0.4292,[72144e]|0.5098,0.5098,[72144e]|0.4476,0.4476,[72144e]|0.422,0.422,[72144e]|0.4017,0.4017,[72144e]|0.3494,0.3494,[72144e]|0.4087,0.4087,[72144e]|
+LINE_GRAPH     IUPredWS (Short)        <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.82,0.82,[329440]|0.7147,0.7147,[329440]|0.6715,0.6715,[329440]|0.6334,0.6334,[329440]|0.59,0.59,[329440]|0.4513,0.4513,[329440]|0.3263,0.3263,[329440]|0.2963,0.2963,[329440]|0.2657,0.2657,[329440]|0.2292,0.2292,[329440]|0.1998,0.1998,[329440]|0.2209,0.2209,[329440]|0.2865,0.2865,[329440]|0.2122,0.2122,[329440]|0.2041,0.2041,[329440]|0.1667,0.1667,[329440]|0.2602,0.2602,[329440]|0.2558,0.2558,[329440]|0.1844,0.1844,[329440]|0.2483,0.2483,[329440]|0.2292,0.2292,[329440]|0.2657,0.2657,[329440]|0.2748,0.2748,[329440]|0.2748,0.2748,[329440]|0.2865,0.2865,[329440]|0.3762,0.3762,[329440]|0.3847,0.3847,[329440]|0.2786,0.2786,[329440]|0.27,0.27,[329440]|0.1878,0.1878,[329440]|0.1805,0.1805,[329440]|0.1805,0.1805,[329440]|0.1532,0.1532,[329440]|0.2255,0.2255,[329440]|0.1958,0.1958,[329440]|0.2786,0.2786,[329440]|0.2657,0.2657,[329440]|0.2748,0.2748,[329440]|0.3491,0.3491,[329440]|0.2531,0.2531,[329440]|0.3456,0.3456,[329440]|0.3491,0.3491,[329440]|0.3146,0.3146,[329440]|0.282,0.282,[329440]|0.27,0.27,[329440]|0.1998,0.1998,[329440]|0.2558,0.2558,[329440]|0.282,0.282,[329440]|0.2602,0.2602,[329440]|0.2602,0.2602,[329440]|0.1878,0.1878,[329440]|0.1844,0.1844,[329440]|0.2122,0.2122,[329440]|0.2292,0.2292,[329440]|0.2602,0.2602,[329440]|0.2786,0.2786,[329440]|0.282,0.282,[329440]|0.3005,0.3005,[329440]|0.2385,0.2385,[329440]|0.3184,0.3184,[329440]|0.2255,0.2255,[329440]|0.2748,0.2748,[329440]|0.3225,0.3225,[329440]|0.3762,0.3762,[329440]|0.3225,0.3225,[329440]|0.3225,0.3225,[329440]|0.2865,0.2865,[329440]|0.2865,0.2865,[329440]|0.3263,0.3263,[329440]|0.3717,0.3717,[329440]|0.4037,0.4037,[329440]|0.4245,0.4245,[329440]|0.4116,0.4116,[329440]|0.3578,0.3578,[329440]|0.3535,0.3535,[329440]|0.2748,0.2748,[329440]|0.2963,0.2963,[329440]|0.2167,0.2167,[329440]|0.3096,0.3096,[329440]|0.2255,0.2255,[329440]|0.3225,0.3225,[329440]|0.1732,0.1732,[329440]|0.1495,0.1495,[329440]|0.1088,0.1088,[329440]|0.1456,0.1456,[329440]|0.2041,0.2041,[329440]|0.1532,0.1532,[329440]|0.2041,0.2041,[329440]|0.1878,0.1878,[329440]|0.1322,0.1322,[329440]|0.1349,0.1349,[329440]|0.1205,0.1205,[329440]|0.0965,0.0965,[329440]|0.0884,0.0884,[329440]|0.0643,0.0643,[329440]|0.0935,0.0935,[329440]|0.0771,0.0771,[329440]|0.1088,0.1088,[329440]|0.0587,0.0587,[329440]|0.0991,0.0991,[329440]|0.0991,0.0991,[329440]|0.1958,0.1958,[329440]|0.2255,0.2255,[329440]|0.2602,0.2602,[329440]|0.2657,0.2657,[329440]|0.1844,0.1844,[329440]|0.2292,0.2292,[329440]|0.2483,0.2483,[329440]|0.2657,0.2657,[329440]|0.3939,0.3939,[329440]|0.4245,0.4245,[329440]|0.4037,0.4037,[329440]|0.4203,0.4203,[329440]|0.4967,0.4967,[329440]|0.5473,0.5473,[329440]|0.4781,0.4781,[329440]|0.4282,0.4282,[329440]|0.3578,0.3578,[329440]|0.4203,0.4203,[329440]|0.3491,0.3491,[329440]|0.2913,0.2913,[329440]|0.2657,0.2657,[329440]|0.1805,0.1805,[329440]|0.2167,0.2167,[329440]|0.208,0.208,[329440]|0.2963,0.2963,[329440]|0.3806,0.3806,[329440]|0.2963,0.2963,[329440]|0.2255,0.2255,[329440]|0.1456,0.1456,[329440]|0.1635,0.1635,[329440]|0.1766,0.1766,[329440]|0.1698,0.1698,[329440]|0.1349,0.1349,[329440]|0.1532,0.1532,[329440]|0.2292,0.2292,[329440]|0.2483,0.2483,[329440]|0.2432,0.2432,[329440]|0.2041,0.2041,[329440]|0.3005,0.3005,[329440]|0.4037,0.4037,[329440]|0.4749,0.4749,[329440]|0.59,0.59,[329440]|0.5941,0.5941,[329440]|0.6442,0.6442,[329440]|0.6827,0.6827,[329440]|0.7034,0.7034,[329440]|0.8001,0.8001,[329440]|
+
+SEQUENCE_REF   Q93Z60_ARATH
+LINE_GRAPH     IUPredWS (Long) <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.1671,0.1671,[72144e]|0.2129,0.2129,[72144e]|0.247,0.247,[72144e]|0.1554,0.1554,[72144e]|0.1162,0.1162,[72144e]|0.1449,0.1449,[72144e]|0.1731,0.1731,[72144e]|0.2064,0.2064,[72144e]|0.2436,0.2436,[72144e]|0.2715,0.2715,[72144e]|0.3215,0.3215,[72144e]|0.2752,0.2752,[72144e]|0.2988,0.2988,[72144e]|0.2364,0.2364,[72144e]|0.2328,0.2328,[72144e]|0.2575,0.2575,[72144e]|0.2575,0.2575,[72144e]|0.2918,0.2918,[72144e]|0.2034,0.2034,[72144e]|0.2034,0.2034,[72144e]|0.2817,0.2817,[72144e]|0.3392,0.3392,[72144e]|0.3494,0.3494,[72144e]|0.3426,0.3426,[72144e]|0.2783,0.2783,[72144e]|0.2752,0.2752,[72144e]|0.3426,0.3426,[72144e]|0.2715,0.2715,[72144e]|0.2609,0.2609,[72144e]|0.247,0.247,[72144e]|0.2364,0.2364,[72144e]|0.2364,0.2364,[72144e]|0.1791,0.1791,[72144e]|0.247,0.247,[72144e]|0.2503,0.2503,[72144e]|0.3215,0.3215,[72144e]|0.3215,0.3215,[72144e]|0.2715,0.2715,[72144e]|0.3426,0.3426,[72144e]|0.2817,0.2817,[72144e]|0.3566,0.3566,[72144e]|0.3566,0.3566,[72144e]|0.3529,0.3529,[72144e]|0.2715,0.2715,[72144e]|0.2575,0.2575,[72144e]|0.2064,0.2064,[72144e]|0.2645,0.2645,[72144e]|0.2645,0.2645,[72144e]|0.1942,0.1942,[72144e]|0.2645,0.2645,[72144e]|0.3053,0.3053,[72144e]|0.3286,0.3286,[72144e]|0.3321,0.3321,[72144e]|0.3494,0.3494,[72144e]|0.384,0.384,[72144e]|0.4051,0.4051,[72144e]|0.3494,0.3494,[72144e]|0.3667,0.3667,[72144e]|0.2752,0.2752,[72144e]|0.346,0.346,[72144e]|0.3631,0.3631,[72144e]|0.4051,0.4051,[72144e]|0.3704,0.3704,[72144e]|0.3215,0.3215,[72144e]|0.268,0.268,[72144e]|0.2783,0.2783,[72144e]|0.2988,0.2988,[72144e]|0.3249,0.3249,[72144e]|0.3053,0.3053,[72144e]|0.422,0.422,[72144e]|0.5139,0.5139,[72144e]|0.4801,0.4801,[72144e]|0.4476,0.4476,[72144e]|0.3566,0.3566,[72144e]|0.374,0.374,[72144e]|0.2849,0.2849,[72144e]|0.3087,0.3087,[72144e]|0.2129,0.2129,[72144e]|0.2645,0.2645,[72144e]|0.1583,0.1583,[72144e]|0.247,0.247,[72144e]|0.2002,0.2002,[72144e]|0.1852,0.1852,[72144e]|0.1702,0.1702,[72144e]|0.1399,0.1399,[72144e]|0.2002,0.2002,[72144e]|0.247,0.247,[72144e]|0.2224,0.2224,[72144e]|0.1852,0.1852,[72144e]|0.2094,0.2094,[72144e]|0.2258,0.2258,[72144e]|0.1611,0.1611,[72144e]|0.1092,0.1092,[72144e]|0.1251,0.1251,[72144e]|0.1251,0.1251,[72144e]|0.1759,0.1759,[72144e]|0.1115,0.1115,[72144e]|0.1731,0.1731,[72144e]|0.1501,0.1501,[72144e]|0.2129,0.2129,[72144e]|0.2292,0.2292,[72144e]|0.3249,0.3249,[72144e]|0.3215,0.3215,[72144e]|0.2645,0.2645,[72144e]|0.2002,0.2002,[72144e]|0.2193,0.2193,[72144e]|0.3286,0.3286,[72144e]|0.3249,0.3249,[72144e]|0.3117,0.3117,[72144e]|0.391,0.391,[72144e]|0.4051,0.4051,[72144e]|0.384,0.384,[72144e]|0.3774,0.3774,[72144e]|0.4292,0.4292,[72144e]|0.4901,0.4901,[72144e]|0.4801,0.4801,[72144e]|0.4582,0.4582,[72144e]|0.4409,0.4409,[72144e]|
+LINE_GRAPH     IUPredWS (Short)        <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.82,0.82,[329440]|0.7147,0.7147,[329440]|0.6715,0.6715,[329440]|0.6334,0.6334,[329440]|0.59,0.59,[329440]|0.4513,0.4513,[329440]|0.3263,0.3263,[329440]|0.2963,0.2963,[329440]|0.2657,0.2657,[329440]|0.2292,0.2292,[329440]|0.1998,0.1998,[329440]|0.2209,0.2209,[329440]|0.2865,0.2865,[329440]|0.2122,0.2122,[329440]|0.2041,0.2041,[329440]|0.1667,0.1667,[329440]|0.2602,0.2602,[329440]|0.2558,0.2558,[329440]|0.1844,0.1844,[329440]|0.2483,0.2483,[329440]|0.2292,0.2292,[329440]|0.2657,0.2657,[329440]|0.2748,0.2748,[329440]|0.2748,0.2748,[329440]|0.2865,0.2865,[329440]|0.3762,0.3762,[329440]|0.3847,0.3847,[329440]|0.2786,0.2786,[329440]|0.27,0.27,[329440]|0.1878,0.1878,[329440]|0.1805,0.1805,[329440]|0.1805,0.1805,[329440]|0.1532,0.1532,[329440]|0.2255,0.2255,[329440]|0.1958,0.1958,[329440]|0.2786,0.2786,[329440]|0.2657,0.2657,[329440]|0.2748,0.2748,[329440]|0.3491,0.3491,[329440]|0.2531,0.2531,[329440]|0.3456,0.3456,[329440]|0.3491,0.3491,[329440]|0.3146,0.3146,[329440]|0.282,0.282,[329440]|0.27,0.27,[329440]|0.1998,0.1998,[329440]|0.2558,0.2558,[329440]|0.282,0.282,[329440]|0.2602,0.2602,[329440]|0.2602,0.2602,[329440]|0.1878,0.1878,[329440]|0.1844,0.1844,[329440]|0.2122,0.2122,[329440]|0.2292,0.2292,[329440]|0.2602,0.2602,[329440]|0.2786,0.2786,[329440]|0.282,0.282,[329440]|0.3005,0.3005,[329440]|0.2385,0.2385,[329440]|0.3184,0.3184,[329440]|0.2255,0.2255,[329440]|0.2748,0.2748,[329440]|0.3225,0.3225,[329440]|0.3762,0.3762,[329440]|0.3225,0.3225,[329440]|0.3225,0.3225,[329440]|0.2865,0.2865,[329440]|0.2865,0.2865,[329440]|0.3263,0.3263,[329440]|0.3717,0.3717,[329440]|0.4037,0.4037,[329440]|0.4245,0.4245,[329440]|0.4116,0.4116,[329440]|0.3578,0.3578,[329440]|0.3535,0.3535,[329440]|0.2748,0.2748,[329440]|0.2963,0.2963,[329440]|0.2167,0.2167,[329440]|0.3096,0.3096,[329440]|0.2255,0.2255,[329440]|0.3225,0.3225,[329440]|0.1732,0.1732,[329440]|0.1495,0.1495,[329440]|0.1088,0.1088,[329440]|0.1456,0.1456,[329440]|0.2041,0.2041,[329440]|0.1532,0.1532,[329440]|0.1998,0.1998,[329440]|0.1844,0.1844,[329440]|0.1205,0.1205,[329440]|0.124,0.124,[329440]|0.1088,0.1088,[329440]|0.0858,0.0858,[329440]|0.0789,0.0789,[329440]|0.0607,0.0607,[329440]|0.0858,0.0858,[329440]|0.0701,0.0701,[329440]|0.1018,0.1018,[329440]|0.0567,0.0567,[329440]|0.0935,0.0935,[329440]|0.0965,0.0965,[329440]|0.1921,0.1921,[329440]|0.2167,0.2167,[329440]|0.2558,0.2558,[329440]|0.2602,0.2602,[329440]|0.1921,0.1921,[329440]|0.2602,0.2602,[329440]|0.2786,0.2786,[329440]|0.2913,0.2913,[329440]|0.4556,0.4556,[329440]|0.5331,0.5331,[329440]|0.5802,0.5802,[329440]|0.6412,0.6412,[329440]|0.7232,0.7232,[329440]|0.8074,0.8074,[329440]|0.8457,0.8457,[329440]|0.8823,0.8823,[329440]|0.9141,0.9141,[329440]|
+
+SEQUENCE_REF   FER1_ARATH
+LINE_GRAPH     IUPredWS (Long) <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.1583,0.1583,[72144e]|0.2034,0.2034,[72144e]|0.2364,0.2364,[72144e]|0.1476,0.1476,[72144e]|0.1048,0.1048,[72144e]|0.1349,0.1349,[72144e]|0.1643,0.1643,[72144e]|0.1881,0.1881,[72144e]|0.247,0.247,[72144e]|0.2399,0.2399,[72144e]|0.2951,0.2951,[72144e]|0.2503,0.2503,[72144e]|0.2783,0.2783,[72144e]|0.2129,0.2129,[72144e]|0.2094,0.2094,[72144e]|0.2364,0.2364,[72144e]|0.2328,0.2328,[72144e]|0.2715,0.2715,[72144e]|0.2715,0.2715,[72144e]|0.2715,0.2715,[72144e]|0.346,0.346,[72144e]|0.4051,0.4051,[72144e]|0.4149,0.4149,[72144e]|0.4087,0.4087,[72144e]|0.3392,0.3392,[72144e]|0.3392,0.3392,[72144e]|0.4087,0.4087,[72144e]|0.3321,0.3321,[72144e]|0.3215,0.3215,[72144e]|0.3215,0.3215,[72144e]|0.2884,0.2884,[72144e]|0.3215,0.3215,[72144e]|0.2609,0.2609,[72144e]|0.3321,0.3321,[72144e]|0.3356,0.3356,[72144e]|0.4051,0.4051,[72144e]|0.4017,0.4017,[72144e]|0.3494,0.3494,[72144e]|0.4292,0.4292,[72144e]|0.3667,0.3667,[72144e]|0.346,0.346,[72144e]|0.3494,0.3494,[72144e]|0.346,0.346,[72144e]|0.268,0.268,[72144e]|0.247,0.247,[72144e]|0.1969,0.1969,[72144e]|0.2541,0.2541,[72144e]|0.2541,0.2541,[72144e]|0.1881,0.1881,[72144e]|0.2609,0.2609,[72144e]|0.3019,0.3019,[72144e]|0.3249,0.3249,[72144e]|0.3249,0.3249,[72144e]|0.346,0.346,[72144e]|0.3053,0.3053,[72144e]|0.3249,0.3249,[72144e]|0.2715,0.2715,[72144e]|0.2951,0.2951,[72144e]|0.2034,0.2034,[72144e]|0.2715,0.2715,[72144e]|0.2817,0.2817,[72144e]|0.3249,0.3249,[72144e]|0.2951,0.2951,[72144e]|0.247,0.247,[72144e]|0.1942,0.1942,[72144e]|0.2002,0.2002,[72144e]|0.2224,0.2224,[72144e]|0.2503,0.2503,[72144e]|0.2328,0.2328,[72144e]|0.346,0.346,[72144e]|0.4409,0.4409,[72144e]|0.4087,0.4087,[72144e]|0.3774,0.3774,[72144e]|0.2849,0.2849,[72144e]|0.2988,0.2988,[72144e]|0.2064,0.2064,[72144e]|0.3087,0.3087,[72144e]|0.2094,0.2094,[72144e]|0.2645,0.2645,[72144e]|0.1554,0.1554,[72144e]|0.2399,0.2399,[72144e]|0.1969,0.1969,[72144e]|0.1852,0.1852,[72144e]|0.1702,0.1702,[72144e]|0.1399,0.1399,[72144e]|0.2002,0.2002,[72144e]|0.2503,0.2503,[72144e]|0.2258,0.2258,[72144e]|0.1881,0.1881,[72144e]|0.2129,0.2129,[72144e]|0.2292,0.2292,[72144e]|0.1611,0.1611,[72144e]|0.107,0.107,[72144e]|0.1251,0.1251,[72144e]|0.1229,0.1229,[72144e]|0.1759,0.1759,[72144e]|0.1229,0.1229,[72144e]|0.1914,0.1914,[72144e]|0.1702,0.1702,[72144e]|0.2364,0.2364,[72144e]|0.2503,0.2503,[72144e]|0.3529,0.3529,[72144e]|0.3494,0.3494,[72144e]|0.2884,0.2884,[72144e]|0.2258,0.2258,[72144e]|0.2436,0.2436,[72144e]|0.3529,0.3529,[72144e]|0.3774,0.3774,[72144e]|0.3872,0.3872,[72144e]|0.4119,0.4119,[72144e]|0.4369,0.4369,[72144e]|0.4619,0.4619,[72144e]|0.4725,0.4725,[72144e]|0.433,0.433,[72144e]|0.4369,0.4369,[72144e]|0.374,0.374,[72144e]|0.3774,0.3774,[72144e]|0.2817,0.2817,[72144e]|0.3087,0.3087,[72144e]|0.2715,0.2715,[72144e]|0.1942,0.1942,[72144e]|0.2292,0.2292,[72144e]|0.2164,0.2164,[72144e]|0.2064,0.2064,[72144e]|0.2224,0.2224,[72144e]|0.2609,0.2609,[72144e]|0.3249,0.3249,[72144e]|0.2436,0.2436,[72144e]|0.2503,0.2503,[72144e]|0.2328,0.2328,[72144e]|0.2193,0.2193,[72144e]|0.2715,0.2715,[72144e]|0.2951,0.2951,[72144e]|0.2988,0.2988,[72144e]|0.3149,0.3149,[72144e]|0.3392,0.3392,[72144e]|0.3356,0.3356,[72144e]|0.3948,0.3948,[72144e]|0.3774,0.3774,[72144e]|0.4725,0.4725,[72144e]|0.4864,0.4864,[72144e]|0.5055,0.5055,[72144e]|0.6043,0.6043,[72144e]|0.5296,0.5296,[72144e]|0.5098,0.5098,[72144e]|0.4979,0.4979,[72144e]|0.4507,0.4507,[72144e]|0.5296,0.5296,[72144e]|
+LINE_GRAPH     IUPredWS (Short)        <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.8242,0.8242,[329440]|0.7275,0.7275,[329440]|0.6906,0.6906,[329440]|0.6516,0.6516,[329440]|0.6124,0.6124,[329440]|0.4781,0.4781,[329440]|0.3535,0.3535,[329440]|0.3225,0.3225,[329440]|0.2913,0.2913,[329440]|0.2432,0.2432,[329440]|0.2292,0.2292,[329440]|0.2209,0.2209,[329440]|0.2913,0.2913,[329440]|0.2167,0.2167,[329440]|0.208,0.208,[329440]|0.1766,0.1766,[329440]|0.2657,0.2657,[329440]|0.2657,0.2657,[329440]|0.1958,0.1958,[329440]|0.2558,0.2558,[329440]|0.3184,0.3184,[329440]|0.3456,0.3456,[329440]|0.3456,0.3456,[329440]|0.3399,0.3399,[329440]|0.3578,0.3578,[329440]|0.4458,0.4458,[329440]|0.46,0.46,[329440]|0.3578,0.3578,[329440]|0.3456,0.3456,[329440]|0.2786,0.2786,[329440]|0.2558,0.2558,[329440]|0.2913,0.2913,[329440]|0.2602,0.2602,[329440]|0.3399,0.3399,[329440]|0.3096,0.3096,[329440]|0.3885,0.3885,[329440]|0.3717,0.3717,[329440]|0.3762,0.3762,[329440]|0.4556,0.4556,[329440]|0.363,0.363,[329440]|0.3668,0.3668,[329440]|0.3668,0.3668,[329440]|0.3359,0.3359,[329440]|0.3005,0.3005,[329440]|0.282,0.282,[329440]|0.208,0.208,[329440]|0.2602,0.2602,[329440]|0.282,0.282,[329440]|0.2602,0.2602,[329440]|0.2483,0.2483,[329440]|0.1732,0.1732,[329440]|0.1698,0.1698,[329440]|0.1998,0.1998,[329440]|0.2122,0.2122,[329440]|0.2432,0.2432,[329440]|0.2602,0.2602,[329440]|0.1878,0.1878,[329440]|0.208,0.208,[329440]|0.1532,0.1532,[329440]|0.2209,0.2209,[329440]|0.1456,0.1456,[329440]|0.1844,0.1844,[329440]|0.2255,0.2255,[329440]|0.2748,0.2748,[329440]|0.2209,0.2209,[329440]|0.2255,0.2255,[329440]|0.1878,0.1878,[329440]|0.1844,0.1844,[329440]|0.2167,0.2167,[329440]|0.2657,0.2657,[329440]|0.3005,0.3005,[329440]|0.3225,0.3225,[329440]|0.3096,0.3096,[329440]|0.2483,0.2483,[329440]|0.2483,0.2483,[329440]|0.1698,0.1698,[329440]|0.2602,0.2602,[329440]|0.1805,0.1805,[329440]|0.27,0.27,[329440]|0.1878,0.1878,[329440]|0.2786,0.2786,[329440]|0.138,0.138,[329440]|0.1205,0.1205,[329440]|0.0884,0.0884,[329440]|0.1178,0.1178,[329440]|0.1732,0.1732,[329440]|0.1292,0.1292,[329440]|0.1805,0.1805,[329440]|0.1698,0.1698,[329440]|0.1178,0.1178,[329440]|0.124,0.124,[329440]|0.1088,0.1088,[329440]|0.0858,0.0858,[329440]|0.0771,0.0771,[329440]|0.0554,0.0554,[329440]|0.0832,0.0832,[329440]|0.0677,0.0677,[329440]|0.1018,0.1018,[329440]|0.0554,0.0554,[329440]|0.0965,0.0965,[329440]|0.0965,0.0965,[329440]|0.1921,0.1921,[329440]|0.2167,0.2167,[329440]|0.2558,0.2558,[329440]|0.2602,0.2602,[329440]|0.1844,0.1844,[329440]|0.2333,0.2333,[329440]|0.2531,0.2531,[329440]|0.2657,0.2657,[329440]|0.3992,0.3992,[329440]|0.4333,0.4333,[329440]|0.3762,0.3762,[329440]|0.3992,0.3992,[329440]|0.4781,0.4781,[329440]|0.5374,0.5374,[329440]|0.4651,0.4651,[329440]|0.4203,0.4203,[329440]|0.3535,0.3535,[329440]|0.4078,0.4078,[329440]|0.3311,0.3311,[329440]|0.3096,0.3096,[329440]|0.2865,0.2865,[329440]|0.208,0.208,[329440]|0.2531,0.2531,[329440]|0.2483,0.2483,[329440]|0.3263,0.3263,[329440]|0.4078,0.4078,[329440]|0.3225,0.3225,[329440]|0.3005,0.3005,[329440]|0.2041,0.2041,[329440]|0.2255,0.2255,[329440]|0.2748,0.2748,[329440]|0.2602,0.2602,[329440]|0.208,0.208,[329440]|0.2292,0.2292,[329440]|0.3263,0.3263,[329440]|0.3885,0.3885,[329440]|0.3939,0.3939,[329440]|0.3456,0.3456,[329440]|0.4458,0.4458,[329440]|0.5173,0.5173,[329440]|0.5802,0.5802,[329440]|0.6789,0.6789,[329440]|0.6789,0.6789,[329440]|0.7275,0.7275,[329440]|0.7644,0.7644,[329440]|0.7912,0.7912,[329440]|0.8823,0.8823,[329440]|
+
+SEQUENCE_REF   FER_BRANA
+LINE_GRAPH     IUPredWS (Long) <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.1969,0.1969,[72144e]|0.2783,0.2783,[72144e]|0.3182,0.3182,[72144e]|0.384,0.384,[72144e]|0.3321,0.3321,[72144e]|0.3872,0.3872,[72144e]|0.2752,0.2752,[72144e]|0.3182,0.3182,[72144e]|0.3599,0.3599,[72144e]|0.3948,0.3948,[72144e]|0.3566,0.3566,[72144e]|0.3149,0.3149,[72144e]|0.2609,0.2609,[72144e]|0.268,0.268,[72144e]|0.3053,0.3053,[72144e]|0.3321,0.3321,[72144e]|0.3249,0.3249,[72144e]|0.4476,0.4476,[72144e]|0.5456,0.5456,[72144e]|0.5098,0.5098,[72144e]|0.4766,0.4766,[72144e]|0.384,0.384,[72144e]|0.4017,0.4017,[72144e]|0.3087,0.3087,[72144e]|0.3321,0.3321,[72144e]|0.2399,0.2399,[72144e]|0.2918,0.2918,[72144e]|0.1643,0.1643,[72144e]|0.2541,0.2541,[72144e]|0.2094,0.2094,[72144e]|0.1942,0.1942,[72144e]|0.1759,0.1759,[72144e]|0.1323,0.1323,[72144e]|0.1852,0.1852,[72144e]|0.2292,0.2292,[72144e]|0.1914,0.1914,[72144e]|0.1528,0.1528,[72144e]|0.1759,0.1759,[72144e]|0.1791,0.1791,[72144e]|0.1206,0.1206,[72144e]|0.0765,0.0765,[72144e]|0.0888,0.0888,[72144e]|0.0888,0.0888,[72144e]|0.0749,0.0749,[72144e]|0.0473,0.0473,[72144e]|0.0817,0.0817,[72144e]|0.0704,0.0704,[72144e]|0.1048,0.1048,[72144e]|0.1162,0.1162,[72144e]|0.2258,0.2258,[72144e]|0.2364,0.2364,[72144e]|0.1731,0.1731,[72144e]|0.1251,0.1251,[72144e]|0.1399,0.1399,[72144e]|0.2503,0.2503,[72144e]|0.2715,0.2715,[72144e]|0.2783,0.2783,[72144e]|0.3215,0.3215,[72144e]|0.3215,0.3215,[72144e]|0.346,0.346,[72144e]|0.3667,0.3667,[72144e]|0.3249,0.3249,[72144e]|0.3249,0.3249,[72144e]|0.2645,0.2645,[72144e]|0.268,0.268,[72144e]|0.2541,0.2541,[72144e]|0.2817,0.2817,[72144e]|0.2399,0.2399,[72144e]|0.1702,0.1702,[72144e]|0.2034,0.2034,[72144e]|0.1914,0.1914,[72144e]|0.1643,0.1643,[72144e]|0.1823,0.1823,[72144e]|0.2164,0.2164,[72144e]|0.2849,0.2849,[72144e]|0.2002,0.2002,[72144e]|0.2064,0.2064,[72144e]|0.1942,0.1942,[72144e]|0.1823,0.1823,[72144e]|0.2224,0.2224,[72144e]|0.2752,0.2752,[72144e]|0.2752,0.2752,[72144e]|0.2988,0.2988,[72144e]|0.3249,0.3249,[72144e]|0.3249,0.3249,[72144e]|0.3872,0.3872,[72144e]|0.3667,0.3667,[72144e]|0.4685,0.4685,[72144e]|0.4864,0.4864,[72144e]|0.5017,0.5017,[72144e]|0.5951,0.5951,[72144e]|0.5296,0.5296,[72144e]|0.5055,0.5055,[72144e]|0.494,0.494,[72144e]|0.4441,0.4441,[72144e]|0.5254,0.5254,[72144e]|
+LINE_GRAPH     IUPredWS (Short)        <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.7605,0.7605,[329440]|0.7458,0.7458,[329440]|0.7079,0.7079,[329440]|0.6906,0.6906,[329440]|0.6557,0.6557,[329440]|0.6412,0.6412,[329440]|0.5374,0.5374,[329440]|0.5173,0.5173,[329440]|0.3806,0.3806,[329440]|0.3578,0.3578,[329440]|0.3311,0.3311,[329440]|0.3885,0.3885,[329440]|0.3456,0.3456,[329440]|0.3456,0.3456,[329440]|0.3225,0.3225,[329440]|0.3225,0.3225,[329440]|0.3806,0.3806,[329440]|0.4116,0.4116,[329440]|0.4379,0.4379,[329440]|0.4651,0.4651,[329440]|0.4458,0.4458,[329440]|0.3806,0.3806,[329440]|0.3762,0.3762,[329440]|0.2913,0.2913,[329440]|0.3096,0.3096,[329440]|0.2167,0.2167,[329440]|0.3146,0.3146,[329440]|0.2255,0.2255,[329440]|0.3184,0.3184,[329440]|0.1698,0.1698,[329440]|0.138,0.138,[329440]|0.1018,0.1018,[329440]|0.1322,0.1322,[329440]|0.1805,0.1805,[329440]|0.1322,0.1322,[329440]|0.1805,0.1805,[329440]|0.1667,0.1667,[329440]|0.1117,0.1117,[329440]|0.115,0.115,[329440]|0.1018,0.1018,[329440]|0.0771,0.0771,[329440]|0.066,0.066,[329440]|0.0478,0.0478,[329440]|0.0677,0.0677,[329440]|0.0554,0.0554,[329440]|0.0478,0.0478,[329440]|0.0268,0.0268,[329440]|0.0441,0.0441,[329440]|0.0455,0.0455,[329440]|0.1018,0.1018,[329440]|0.124,0.124,[329440]|0.1667,0.1667,[329440]|0.1698,0.1698,[329440]|0.1088,0.1088,[329440]|0.138,0.138,[329440]|0.1532,0.1532,[329440]|0.1667,0.1667,[329440]|0.2786,0.2786,[329440]|0.3184,0.3184,[329440]|0.2602,0.2602,[329440]|0.2558,0.2558,[329440]|0.3399,0.3399,[329440]|0.4078,0.4078,[329440]|0.3263,0.3263,[329440]|0.2786,0.2786,[329440]|0.2913,0.2913,[329440]|0.3491,0.3491,[329440]|0.27,0.27,[329440]|0.2432,0.2432,[329440]|0.2209,0.2209,[329440]|0.1532,0.1532,[329440]|0.1732,0.1732,[329440]|0.1698,0.1698,[329440]|0.2483,0.2483,[329440]|0.3311,0.3311,[329440]|0.2483,0.2483,[329440]|0.2292,0.2292,[329440]|0.1495,0.1495,[329440]|0.1698,0.1698,[329440]|0.2122,0.2122,[329440]|0.2292,0.2292,[329440]|0.1805,0.1805,[329440]|0.1998,0.1998,[329440]|0.3053,0.3053,[329440]|0.3806,0.3806,[329440]|0.3939,0.3939,[329440]|0.3399,0.3399,[329440]|0.4513,0.4513,[329440]|0.5173,0.5173,[329440]|0.5846,0.5846,[329440]|0.6827,0.6827,[329440]|0.6827,0.6827,[329440]|0.7317,0.7317,[329440]|0.7688,0.7688,[329440]|0.7951,0.7951,[329440]|0.8857,0.8857,[329440]|
+
+SEQUENCE_REF   FER3_RAPSA
+LINE_GRAPH     IUPredWS (Long) <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.2224,0.2224,[72144e]|0.3053,0.3053,[72144e]|0.346,0.346,[72144e]|0.4087,0.4087,[72144e]|0.3599,0.3599,[72144e]|0.4149,0.4149,[72144e]|0.2988,0.2988,[72144e]|0.3426,0.3426,[72144e]|0.384,0.384,[72144e]|0.4186,0.4186,[72144e]|0.384,0.384,[72144e]|0.3426,0.3426,[72144e]|0.2918,0.2918,[72144e]|0.2988,0.2988,[72144e]|0.3356,0.3356,[72144e]|0.3599,0.3599,[72144e]|0.3529,0.3529,[72144e]|0.4685,0.4685,[72144e]|0.5665,0.5665,[72144e]|0.5342,0.5342,[72144e]|0.4979,0.4979,[72144e]|0.4087,0.4087,[72144e]|0.4256,0.4256,[72144e]|0.3356,0.3356,[72144e]|0.3599,0.3599,[72144e]|0.268,0.268,[72144e]|0.3182,0.3182,[72144e]|0.1881,0.1881,[72144e]|0.2849,0.2849,[72144e]|0.2399,0.2399,[72144e]|0.2224,0.2224,[72144e]|0.2034,0.2034,[72144e]|0.1528,0.1528,[72144e]|0.2094,0.2094,[72144e]|0.2575,0.2575,[72144e]|0.2129,0.2129,[72144e]|0.1759,0.1759,[72144e]|0.1969,0.1969,[72144e]|0.2034,0.2034,[72144e]|0.1424,0.1424,[72144e]|0.0929,0.0929,[72144e]|0.107,0.107,[72144e]|0.107,0.107,[72144e]|0.1501,0.1501,[72144e]|0.1028,0.1028,[72144e]|0.1611,0.1611,[72144e]|0.1399,0.1399,[72144e]|0.1942,0.1942,[72144e]|0.2129,0.2129,[72144e]|0.3249,0.3249,[72144e]|0.3321,0.3321,[72144e]|0.2715,0.2715,[72144e]|0.2094,0.2094,[72144e]|0.2258,0.2258,[72144e]|0.3529,0.3529,[72144e]|0.374,0.374,[72144e]|0.3807,0.3807,[72144e]|0.4256,0.4256,[72144e]|0.4256,0.4256,[72144e]|0.4507,0.4507,[72144e]|0.4685,0.4685,[72144e]|0.4256,0.4256,[72144e]|0.4292,0.4292,[72144e]|0.3667,0.3667,[72144e]|0.3704,0.3704,[72144e]|0.2645,0.2645,[72144e]|0.2918,0.2918,[72144e]|0.2503,0.2503,[72144e]|0.1823,0.1823,[72144e]|0.2129,0.2129,[72144e]|0.2002,0.2002,[72144e]|0.1914,0.1914,[72144e]|0.2094,0.2094,[72144e]|0.247,0.247,[72144e]|0.3117,0.3117,[72144e]|0.2292,0.2292,[72144e]|0.2328,0.2328,[72144e]|0.2193,0.2193,[72144e]|0.2064,0.2064,[72144e]|0.2609,0.2609,[72144e]|0.3087,0.3087,[72144e]|0.3087,0.3087,[72144e]|0.3286,0.3286,[72144e]|0.3983,0.3983,[72144e]|0.3948,0.3948,[72144e]|0.4541,0.4541,[72144e]|0.4369,0.4369,[72144e]|0.5533,0.5533,[72144e]|0.5758,0.5758,[72144e]|0.5992,0.5992,[72144e]|0.708,0.708,[72144e]|0.6375,0.6375,[72144e]|0.6227,0.6227,[72144e]|0.6136,0.6136,[72144e]|0.5577,0.5577,[72144e]|0.6661,0.6661,[72144e]|
+LINE_GRAPH     IUPredWS (Short)        <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.7605,0.7605,[329440]|0.7458,0.7458,[329440]|0.7079,0.7079,[329440]|0.6906,0.6906,[329440]|0.6557,0.6557,[329440]|0.6412,0.6412,[329440]|0.5374,0.5374,[329440]|0.5173,0.5173,[329440]|0.3806,0.3806,[329440]|0.3578,0.3578,[329440]|0.3311,0.3311,[329440]|0.3885,0.3885,[329440]|0.3456,0.3456,[329440]|0.3456,0.3456,[329440]|0.3225,0.3225,[329440]|0.3225,0.3225,[329440]|0.3806,0.3806,[329440]|0.4116,0.4116,[329440]|0.4379,0.4379,[329440]|0.4651,0.4651,[329440]|0.4458,0.4458,[329440]|0.3806,0.3806,[329440]|0.3806,0.3806,[329440]|0.2963,0.2963,[329440]|0.3184,0.3184,[329440]|0.2292,0.2292,[329440]|0.3225,0.3225,[329440]|0.2385,0.2385,[329440]|0.3359,0.3359,[329440]|0.1844,0.1844,[329440]|0.1566,0.1566,[329440]|0.115,0.115,[329440]|0.1495,0.1495,[329440]|0.2041,0.2041,[329440]|0.1532,0.1532,[329440]|0.2041,0.2041,[329440]|0.1878,0.1878,[329440]|0.1322,0.1322,[329440]|0.1349,0.1349,[329440]|0.1205,0.1205,[329440]|0.0965,0.0965,[329440]|0.0832,0.0832,[329440]|0.0607,0.0607,[329440]|0.0858,0.0858,[329440]|0.0701,0.0701,[329440]|0.1018,0.1018,[329440]|0.0554,0.0554,[329440]|0.0909,0.0909,[329440]|0.0909,0.0909,[329440]|0.1844,0.1844,[329440]|0.208,0.208,[329440]|0.2483,0.2483,[329440]|0.2531,0.2531,[329440]|0.1732,0.1732,[329440]|0.2167,0.2167,[329440]|0.2333,0.2333,[329440]|0.2483,0.2483,[329440]|0.3717,0.3717,[329440]|0.4078,0.4078,[329440]|0.3535,0.3535,[329440]|0.3456,0.3456,[329440]|0.4282,0.4282,[329440]|0.4879,0.4879,[329440]|0.4116,0.4116,[329440]|0.3668,0.3668,[329440]|0.3005,0.3005,[329440]|0.3578,0.3578,[329440]|0.282,0.282,[329440]|0.2558,0.2558,[329440]|0.2385,0.2385,[329440]|0.1667,0.1667,[329440]|0.2041,0.2041,[329440]|0.1998,0.1998,[329440]|0.282,0.282,[329440]|0.363,0.363,[329440]|0.282,0.282,[329440]|0.2602,0.2602,[329440]|0.1766,0.1766,[329440]|0.1998,0.1998,[329440]|0.2483,0.2483,[329440]|0.2657,0.2657,[329440]|0.2255,0.2255,[329440]|0.2531,0.2531,[329440]|0.3491,0.3491,[329440]|0.4116,0.4116,[329440]|0.4458,0.4458,[329440]|0.3992,0.3992,[329440]|0.5008,0.5008,[329440]|0.5623,0.5623,[329440]|0.6293,0.6293,[329440]|0.7275,0.7275,[329440]|0.7275,0.7275,[329440]|0.7724,0.7724,[329440]|0.8118,0.8118,[329440]|0.8391,0.8391,[329440]|0.9141,0.9141,[329440]|
+
+SEQUENCE_REF   FER1_MAIZE
+LINE_GRAPH     IUPredWS (Long) <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.422,0.422,[72144e]|0.2918,0.2918,[72144e]|0.1852,0.1852,[72144e]|0.1115,0.1115,[72144e]|0.1373,0.1373,[72144e]|0.1643,0.1643,[72144e]|0.1914,0.1914,[72144e]|0.2193,0.2193,[72144e]|0.1731,0.1731,[72144e]|0.2002,0.2002,[72144e]|0.1969,0.1969,[72144e]|0.1969,0.1969,[72144e]|0.2575,0.2575,[72144e]|0.2193,0.2193,[72144e]|0.3087,0.3087,[72144e]|0.384,0.384,[72144e]|0.3566,0.3566,[72144e]|0.3019,0.3019,[72144e]|0.2436,0.2436,[72144e]|0.1731,0.1731,[72144e]|0.2292,0.2292,[72144e]|0.1759,0.1759,[72144e]|0.1759,0.1759,[72144e]|0.2575,0.2575,[72144e]|0.2918,0.2918,[72144e]|0.384,0.384,[72144e]|0.3117,0.3117,[72144e]|0.2817,0.2817,[72144e]|0.2849,0.2849,[72144e]|0.2849,0.2849,[72144e]|0.3529,0.3529,[72144e]|0.3215,0.3215,[72144e]|0.3494,0.3494,[72144e]|0.374,0.374,[72144e]|0.3426,0.3426,[72144e]|0.374,0.374,[72144e]|0.3426,0.3426,[72144e]|0.268,0.268,[72144e]|0.2951,0.2951,[72144e]|0.3249,0.3249,[72144e]|0.3631,0.3631,[72144e]|0.4087,0.4087,[72144e]|0.384,0.384,[72144e]|0.3321,0.3321,[72144e]|0.3704,0.3704,[72144e]|0.3215,0.3215,[72144e]|0.3704,0.3704,[72144e]|0.3019,0.3019,[72144e]|0.3053,0.3053,[72144e]|0.3392,0.3392,[72144e]|0.3704,0.3704,[72144e]|0.3872,0.3872,[72144e]|0.391,0.391,[72144e]|0.4409,0.4409,[72144e]|0.3872,0.3872,[72144e]|0.4087,0.4087,[72144e]|0.3392,0.3392,[72144e]|0.3494,0.3494,[72144e]|0.2951,0.2951,[72144e]|0.3948,0.3948,[72144e]|0.4119,0.4119,[72144e]|0.4582,0.4582,[72144e]|0.391,0.391,[72144e]|0.3426,0.3426,[72144e]|0.2645,0.2645,[72144e]|0.2783,0.2783,[72144e]|0.2849,0.2849,[72144e]|0.3494,0.3494,[72144e]|0.3286,0.3286,[72144e]|0.4149,0.4149,[72144e]|0.5139,0.5139,[72144e]|0.5296,0.5296,[72144e]|0.494,0.494,[72144e]|0.3983,0.3983,[72144e]|0.4119,0.4119,[72144e]|0.3215,0.3215,[72144e]|0.4087,0.4087,[72144e]|0.3087,0.3087,[72144e]|0.3774,0.3774,[72144e]|0.2817,0.2817,[72144e]|0.3356,0.3356,[72144e]|0.2817,0.2817,[72144e]|0.2645,0.2645,[72144e]|0.247,0.247,[72144e]|0.2164,0.2164,[72144e]|0.2918,0.2918,[72144e]|0.3631,0.3631,[72144e]|0.346,0.346,[72144e]|0.3019,0.3019,[72144e]|0.2951,0.2951,[72144e]|0.3117,0.3117,[72144e]|0.2399,0.2399,[72144e]|0.1702,0.1702,[72144e]|0.1554,0.1554,[72144e]|0.1554,0.1554,[72144e]|0.2193,0.2193,[72144e]|0.1554,0.1554,[72144e]|0.2364,0.2364,[72144e]|0.2129,0.2129,[72144e]|0.2918,0.2918,[72144e]|0.3087,0.3087,[72144e]|0.4017,0.4017,[72144e]|0.4017,0.4017,[72144e]|0.3566,0.3566,[72144e]|0.2884,0.2884,[72144e]|0.3087,0.3087,[72144e]|0.4119,0.4119,[72144e]|0.4119,0.4119,[72144e]|0.422,0.422,[72144e]|0.4369,0.4369,[72144e]|0.4409,0.4409,[72144e]|0.4541,0.4541,[72144e]|0.4619,0.4619,[72144e]|0.4409,0.4409,[72144e]|0.4441,0.4441,[72144e]|0.374,0.374,[72144e]|0.3774,0.3774,[72144e]|0.2918,0.2918,[72144e]|0.3494,0.3494,[72144e]|0.3087,0.3087,[72144e]|0.2328,0.2328,[72144e]|0.268,0.268,[72144e]|0.2541,0.2541,[72144e]|0.247,0.247,[72144e]|0.2645,0.2645,[72144e]|0.2849,0.2849,[72144e]|0.3053,0.3053,[72144e]|0.2193,0.2193,[72144e]|0.2224,0.2224,[72144e]|0.2224,0.2224,[72144e]|0.2164,0.2164,[72144e]|0.2752,0.2752,[72144e]|0.3149,0.3149,[72144e]|0.3149,0.3149,[72144e]|0.3356,0.3356,[72144e]|0.346,0.346,[72144e]|0.4017,0.4017,[72144e]|0.4685,0.4685,[72144e]|0.4409,0.4409,[72144e]|0.5296,0.5296,[72144e]|0.5139,0.5139,[72144e]|0.5296,0.5296,[72144e]|0.6136,0.6136,[72144e]|0.5493,0.5493,[72144e]|0.5296,0.5296,[72144e]|0.5139,0.5139,[72144e]|0.4685,0.4685,[72144e]|0.5342,0.5342,[72144e]|0.6136,0.6136,[72144e]|0.7547,0.7547,[72144e]|
+LINE_GRAPH     IUPredWS (Short)        <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.865,0.865,[329440]|0.8488,0.8488,[329440]|0.7724,0.7724,[329440]|0.6557,0.6557,[329440]|0.5253,0.5253,[329440]|0.3847,0.3847,[329440]|0.3399,0.3399,[329440]|0.2913,0.2913,[329440]|0.2432,0.2432,[329440]|0.1958,0.1958,[329440]|0.106,0.106,[329440]|0.1456,0.1456,[329440]|0.1456,0.1456,[329440]|0.115,0.115,[329440]|0.1844,0.1844,[329440]|0.2122,0.2122,[329440]|0.2333,0.2333,[329440]|0.2531,0.2531,[329440]|0.1998,0.1998,[329440]|0.1322,0.1322,[329440]|0.1456,0.1456,[329440]|0.0858,0.0858,[329440]|0.1266,0.1266,[329440]|0.1667,0.1667,[329440]|0.2122,0.2122,[329440]|0.3225,0.3225,[329440]|0.2483,0.2483,[329440]|0.2483,0.2483,[329440]|0.1766,0.1766,[329440]|0.1602,0.1602,[329440]|0.2255,0.2255,[329440]|0.2209,0.2209,[329440]|0.2558,0.2558,[329440]|0.2657,0.2657,[329440]|0.2432,0.2432,[329440]|0.2865,0.2865,[329440]|0.27,0.27,[329440]|0.2748,0.2748,[329440]|0.3146,0.3146,[329440]|0.3184,0.3184,[329440]|0.3491,0.3491,[329440]|0.3847,0.3847,[329440]|0.3668,0.3668,[329440]|0.363,0.363,[329440]|0.4037,0.4037,[329440]|0.3184,0.3184,[329440]|0.4037,0.4037,[329440]|0.3359,0.3359,[329440]|0.4116,0.4116,[329440]|0.3717,0.3717,[329440]|0.3005,0.3005,[329440]|0.2865,0.2865,[329440]|0.3263,0.3263,[329440]|0.3668,0.3668,[329440]|0.3717,0.3717,[329440]|0.3806,0.3806,[329440]|0.3053,0.3053,[329440]|0.3146,0.3146,[329440]|0.2292,0.2292,[329440]|0.3096,0.3096,[329440]|0.2432,0.2432,[329440]|0.3146,0.3146,[329440]|0.3225,0.3225,[329440]|0.3806,0.3806,[329440]|0.3184,0.3184,[329440]|0.3311,0.3311,[329440]|0.2657,0.2657,[329440]|0.2657,0.2657,[329440]|0.2913,0.2913,[329440]|0.3578,0.3578,[329440]|0.3939,0.3939,[329440]|0.4116,0.4116,[329440]|0.3885,0.3885,[329440]|0.4037,0.4037,[329440]|0.3939,0.3939,[329440]|0.3184,0.3184,[329440]|0.4116,0.4116,[329440]|0.3263,0.3263,[329440]|0.4379,0.4379,[329440]|0.363,0.363,[329440]|0.4282,0.4282,[329440]|0.2865,0.2865,[329440]|0.2602,0.2602,[329440]|0.2041,0.2041,[329440]|0.2558,0.2558,[329440]|0.3225,0.3225,[329440]|0.2748,0.2748,[329440]|0.3399,0.3399,[329440]|0.3225,0.3225,[329440]|0.2122,0.2122,[329440]|0.2209,0.2209,[329440]|0.1998,0.1998,[329440]|0.1698,0.1698,[329440]|0.1178,0.1178,[329440]|0.0909,0.0909,[329440]|0.1292,0.1292,[329440]|0.106,0.106,[329440]|0.1532,0.1532,[329440]|0.0935,0.0935,[329440]|0.138,0.138,[329440]|0.138,0.138,[329440]|0.2292,0.2292,[329440]|0.2531,0.2531,[329440]|0.2865,0.2865,[329440]|0.2865,0.2865,[329440]|0.2122,0.2122,[329440]|0.2558,0.2558,[329440]|0.27,0.27,[329440]|0.2786,0.2786,[329440]|0.3847,0.3847,[329440]|0.4203,0.4203,[329440]|0.363,0.363,[329440]|0.3535,0.3535,[329440]|0.4149,0.4149,[329440]|0.4703,0.4703,[329440]|0.3939,0.3939,[329440]|0.3535,0.3535,[329440]|0.2865,0.2865,[329440]|0.3359,0.3359,[329440]|0.2602,0.2602,[329440]|0.2558,0.2558,[329440]|0.2333,0.2333,[329440]|0.1635,0.1635,[329440]|0.1958,0.1958,[329440]|0.1878,0.1878,[329440]|0.2657,0.2657,[329440]|0.3456,0.3456,[329440]|0.2748,0.2748,[329440]|0.2167,0.2167,[329440]|0.1602,0.1602,[329440]|0.1766,0.1766,[329440]|0.2255,0.2255,[329440]|0.2333,0.2333,[329440]|0.1998,0.1998,[329440]|0.2209,0.2209,[329440]|0.3184,0.3184,[329440]|0.3847,0.3847,[329440]|0.3847,0.3847,[329440]|0.3847,0.3847,[329440]|0.4513,0.4513,[329440]|0.4282,0.4282,[329440]|0.4967,0.4967,[329440]|0.6079,0.6079,[329440]|0.6124,0.6124,[329440]|0.6604,0.6604,[329440]|0.6944,0.6944,[329440]|0.7232,0.7232,[329440]|0.8118,0.8118,[329440]|0.8857,0.8857,[329440]|0.9491,0.9491,[329440]|
+
+SEQUENCE_REF   O80429_MAIZE
+LINE_GRAPH     IUPredWS (Long) <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.1007,0.1007,[72144e]|0.1028,0.1028,[72144e]|0.1731,0.1731,[72144e]|0.2503,0.2503,[72144e]|0.3249,0.3249,[72144e]|0.2292,0.2292,[72144e]|0.1476,0.1476,[72144e]|0.1731,0.1731,[72144e]|0.1942,0.1942,[72144e]|0.2503,0.2503,[72144e]|0.1969,0.1969,[72144e]|0.2258,0.2258,[72144e]|0.1823,0.1823,[72144e]|0.2094,0.2094,[72144e]|0.1501,0.1501,[72144e]|0.1501,0.1501,[72144e]|0.1611,0.1611,[72144e]|0.1399,0.1399,[72144e]|0.1554,0.1554,[72144e]|0.1823,0.1823,[72144e]|0.1881,0.1881,[72144e]|0.2258,0.2258,[72144e]|0.1969,0.1969,[72144e]|0.2541,0.2541,[72144e]|0.1942,0.1942,[72144e]|0.1671,0.1671,[72144e]|0.1399,0.1399,[72144e]|0.2292,0.2292,[72144e]|0.2575,0.2575,[72144e]|0.1881,0.1881,[72144e]|0.1881,0.1881,[72144e]|0.1399,0.1399,[72144e]|0.2129,0.2129,[72144e]|0.1852,0.1852,[72144e]|0.2645,0.2645,[72144e]|0.1852,0.1852,[72144e]|0.2503,0.2503,[72144e]|0.2193,0.2193,[72144e]|0.2752,0.2752,[72144e]|0.2292,0.2292,[72144e]|0.1611,0.1611,[72144e]|0.1424,0.1424,[72144e]|0.2364,0.2364,[72144e]|0.2884,0.2884,[72144e]|0.3182,0.3182,[72144e]|0.3087,0.3087,[72144e]|0.2783,0.2783,[72144e]|0.2988,0.2988,[72144e]|0.2224,0.2224,[72144e]|0.2224,0.2224,[72144e]|0.2364,0.2364,[72144e]|0.3392,0.3392,[72144e]|0.3566,0.3566,[72144e]|0.4051,0.4051,[72144e]|0.3356,0.3356,[72144e]|0.2817,0.2817,[72144e]|0.1969,0.1969,[72144e]|0.2094,0.2094,[72144e]|0.2164,0.2164,[72144e]|0.1791,0.1791,[72144e]|0.1583,0.1583,[72144e]|0.2436,0.2436,[72144e]|0.3426,0.3426,[72144e]|0.3566,0.3566,[72144e]|0.3286,0.3286,[72144e]|0.2258,0.2258,[72144e]|0.2436,0.2436,[72144e]|0.1554,0.1554,[72144e]|0.2364,0.2364,[72144e]|0.1298,0.1298,[72144e]|0.1914,0.1914,[72144e]|0.1115,0.1115,[72144e]|0.1528,0.1528,[72144e]|0.1115,0.1115,[72144e]|0.1007,0.1007,[72144e]|0.0909,0.0909,[72144e]|0.0734,0.0734,[72144e]|0.1206,0.1206,[72144e]|0.1823,0.1823,[72144e]|0.1643,0.1643,[72144e]|0.1298,0.1298,[72144e]|0.2164,0.2164,[72144e]|0.2399,0.2399,[72144e]|0.1671,0.1671,[72144e]|0.1092,0.1092,[72144e]|0.0948,0.0948,[72144e]|0.0948,0.0948,[72144e]|0.1501,0.1501,[72144e]|0.0967,0.0967,[72144e]|0.1611,0.1611,[72144e]|0.1424,0.1424,[72144e]|0.2328,0.2328,[72144e]|0.2503,0.2503,[72144e]|0.3529,0.3529,[72144e]|0.3494,0.3494,[72144e]|0.2817,0.2817,[72144e]|0.2064,0.2064,[72144e]|0.2193,0.2193,[72144e]|0.3286,0.3286,[72144e]|0.3392,0.3392,[72144e]|0.3494,0.3494,[72144e]|0.384,0.384,[72144e]|0.3872,0.3872,[72144e]|0.4017,0.4017,[72144e]|0.4087,0.4087,[72144e]|0.3807,0.3807,[72144e]|0.384,0.384,[72144e]|0.3117,0.3117,[72144e]|0.3182,0.3182,[72144e]|0.2328,0.2328,[72144e]|0.268,0.268,[72144e]|0.2258,0.2258,[72144e]|0.1501,0.1501,[72144e]|0.1791,0.1791,[72144e]|0.1702,0.1702,[72144e]|0.1611,0.1611,[72144e]|0.1791,0.1791,[72144e]|0.2164,0.2164,[72144e]|0.2328,0.2328,[72144e]|0.1554,0.1554,[72144e]|0.1583,0.1583,[72144e]|0.1528,0.1528,[72144e]|0.1424,0.1424,[72144e]|0.1823,0.1823,[72144e]|0.2224,0.2224,[72144e]|0.2224,0.2224,[72144e]|0.2436,0.2436,[72144e]|0.2541,0.2541,[72144e]|0.2399,0.2399,[72144e]|0.3087,0.3087,[72144e]|0.2817,0.2817,[72144e]|0.3566,0.3566,[72144e]|0.3667,0.3667,[72144e]|0.3774,0.3774,[72144e]|0.4541,0.4541,[72144e]|0.391,0.391,[72144e]|0.3599,0.3599,[72144e]|0.3356,0.3356,[72144e]|0.2783,0.2783,[72144e]|0.3426,0.3426,[72144e]|
+LINE_GRAPH     IUPredWS (Short)        <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.7573,0.7573,[329440]|0.6516,0.6516,[329440]|0.6293,0.6293,[329440]|0.5412,0.5412,[329440]|0.5229,0.5229,[329440]|0.5008,0.5008,[329440]|0.4825,0.4825,[329440]|0.3806,0.3806,[329440]|0.2292,0.2292,[329440]|0.1921,0.1921,[329440]|0.1602,0.1602,[329440]|0.208,0.208,[329440]|0.1667,0.1667,[329440]|0.2167,0.2167,[329440]|0.1416,0.1416,[329440]|0.1878,0.1878,[329440]|0.1921,0.1921,[329440]|0.1635,0.1635,[329440]|0.1322,0.1322,[329440]|0.1088,0.1088,[329440]|0.1805,0.1805,[329440]|0.2748,0.2748,[329440]|0.1805,0.1805,[329440]|0.1921,0.1921,[329440]|0.1495,0.1495,[329440]|0.1495,0.1495,[329440]|0.1088,0.1088,[329440]|0.1532,0.1532,[329440]|0.2531,0.2531,[329440]|0.2531,0.2531,[329440]|0.1805,0.1805,[329440]|0.106,0.106,[329440]|0.1667,0.1667,[329440]|0.1292,0.1292,[329440]|0.1998,0.1998,[329440]|0.1566,0.1566,[329440]|0.2292,0.2292,[329440]|0.1844,0.1844,[329440]|0.27,0.27,[329440]|0.2255,0.2255,[329440]|0.2041,0.2041,[329440]|0.124,0.124,[329440]|0.1205,0.1205,[329440]|0.1416,0.1416,[329440]|0.1998,0.1998,[329440]|0.1958,0.1958,[329440]|0.2292,0.2292,[329440]|0.2483,0.2483,[329440]|0.1732,0.1732,[329440]|0.1805,0.1805,[329440]|0.1667,0.1667,[329440]|0.2432,0.2432,[329440]|0.1732,0.1732,[329440]|0.2385,0.2385,[329440]|0.2531,0.2531,[329440]|0.3096,0.3096,[329440]|0.2385,0.2385,[329440]|0.2531,0.2531,[329440]|0.1844,0.1844,[329440]|0.1921,0.1921,[329440]|0.2167,0.2167,[329440]|0.208,0.208,[329440]|0.2558,0.2558,[329440]|0.27,0.27,[329440]|0.2558,0.2558,[329440]|0.2558,0.2558,[329440]|0.2531,0.2531,[329440]|0.1732,0.1732,[329440]|0.27,0.27,[329440]|0.1844,0.1844,[329440]|0.3005,0.3005,[329440]|0.208,0.208,[329440]|0.282,0.282,[329440]|0.1456,0.1456,[329440]|0.124,0.124,[329440]|0.0884,0.0884,[329440]|0.1292,0.1292,[329440]|0.1805,0.1805,[329440]|0.1416,0.1416,[329440]|0.1998,0.1998,[329440]|0.1844,0.1844,[329440]|0.1635,0.1635,[329440]|0.1667,0.1667,[329440]|0.1532,0.1532,[329440]|0.124,0.124,[329440]|0.0789,0.0789,[329440]|0.0554,0.0554,[329440]|0.0858,0.0858,[329440]|0.0701,0.0701,[329440]|0.106,0.106,[329440]|0.0587,0.0587,[329440]|0.1088,0.1088,[329440]|0.1088,0.1088,[329440]|0.1878,0.1878,[329440]|0.2122,0.2122,[329440]|0.2483,0.2483,[329440]|0.2432,0.2432,[329440]|0.1667,0.1667,[329440]|0.208,0.208,[329440]|0.2041,0.2041,[329440]|0.2209,0.2209,[329440]|0.3311,0.3311,[329440]|0.3668,0.3668,[329440]|0.3184,0.3184,[329440]|0.3096,0.3096,[329440]|0.3762,0.3762,[329440]|0.4282,0.4282,[329440]|0.3578,0.3578,[329440]|0.3096,0.3096,[329440]|0.2385,0.2385,[329440]|0.2865,0.2865,[329440]|0.2167,0.2167,[329440]|0.1878,0.1878,[329440]|0.1732,0.1732,[329440]|0.115,0.115,[329440]|0.1416,0.1416,[329440]|0.1349,0.1349,[329440]|0.208,0.208,[329440]|0.2865,0.2865,[329440]|0.2255,0.2255,[329440]|0.1667,0.1667,[329440]|0.106,0.106,[329440]|0.1205,0.1205,[329440]|0.1456,0.1456,[329440]|0.1495,0.1495,[329440]|0.1266,0.1266,[329440]|0.1416,0.1416,[329440]|0.208,0.208,[329440]|0.27,0.27,[329440]|0.27,0.27,[329440]|0.208,0.208,[329440]|0.3146,0.3146,[329440]|0.3806,0.3806,[329440]|0.4513,0.4513,[329440]|0.5623,0.5623,[329440]|0.5623,0.5623,[329440]|0.6219,0.6219,[329440]|0.6604,0.6604,[329440]|0.6906,0.6906,[329440]|0.7817,0.7817,[329440]|
+
+SEQUENCE_REF   Q7XA98_TRIPR
+LINE_GRAPH     IUPredWS (Long) <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.2292,0.2292,[72144e]|0.2645,0.2645,[72144e]|0.3019,0.3019,[72144e]|0.3286,0.3286,[72144e]|0.2328,0.2328,[72144e]|0.2258,0.2258,[72144e]|0.2645,0.2645,[72144e]|0.2988,0.2988,[72144e]|0.3286,0.3286,[72144e]|0.3774,0.3774,[72144e]|0.346,0.346,[72144e]|0.4051,0.4051,[72144e]|0.4051,0.4051,[72144e]|0.4017,0.4017,[72144e]|0.3494,0.3494,[72144e]|0.2988,0.2988,[72144e]|0.3286,0.3286,[72144e]|0.3948,0.3948,[72144e]|0.4864,0.4864,[72144e]|0.494,0.494,[72144e]|0.494,0.494,[72144e]|0.5139,0.5139,[72144e]|0.5419,0.5419,[72144e]|0.4441,0.4441,[72144e]|0.4685,0.4685,[72144e]|0.4685,0.4685,[72144e]|0.5707,0.5707,[72144e]|0.4901,0.4901,[72144e]|0.4831,0.4831,[72144e]|0.4087,0.4087,[72144e]|0.3872,0.3872,[72144e]|0.3566,0.3566,[72144e]|0.3566,0.3566,[72144e]|0.3215,0.3215,[72144e]|0.3566,0.3566,[72144e]|0.346,0.346,[72144e]|0.3983,0.3983,[72144e]|0.4256,0.4256,[72144e]|0.4369,0.4369,[72144e]|0.3667,0.3667,[72144e]|0.3392,0.3392,[72144e]|0.2884,0.2884,[72144e]|0.2609,0.2609,[72144e]|0.2436,0.2436,[72144e]|0.2436,0.2436,[72144e]|0.3392,0.3392,[72144e]|0.2328,0.2328,[72144e]|0.2258,0.2258,[72144e]|0.1791,0.1791,[72144e]|0.2575,0.2575,[72144e]|0.1969,0.1969,[72144e]|0.1969,0.1969,[72144e]|0.2094,0.2094,[72144e]|0.2399,0.2399,[72144e]|0.3149,0.3149,[72144e]|0.3182,0.3182,[72144e]|0.3426,0.3426,[72144e]|0.3599,0.3599,[72144e]|0.3807,0.3807,[72144e]|0.2884,0.2884,[72144e]|0.2884,0.2884,[72144e]|0.2609,0.2609,[72144e]|0.3149,0.3149,[72144e]|0.3774,0.3774,[72144e]|0.4119,0.4119,[72144e]|0.391,0.391,[72144e]|0.3356,0.3356,[72144e]|0.268,0.268,[72144e]|0.2849,0.2849,[72144e]|0.3117,0.3117,[72144e]|0.3599,0.3599,[72144e]|0.346,0.346,[72144e]|0.4292,0.4292,[72144e]|0.5254,0.5254,[72144e]|0.4652,0.4652,[72144e]|0.4369,0.4369,[72144e]|0.346,0.346,[72144e]|0.3704,0.3704,[72144e]|0.2783,0.2783,[72144e]|0.2988,0.2988,[72144e]|0.1969,0.1969,[72144e]|0.2849,0.2849,[72144e]|0.1852,0.1852,[72144e]|0.2752,0.2752,[72144e]|0.2193,0.2193,[72144e]|0.2064,0.2064,[72144e]|0.1942,0.1942,[72144e]|0.1583,0.1583,[72144e]|0.2258,0.2258,[72144e]|0.2918,0.2918,[72144e]|0.2609,0.2609,[72144e]|0.2224,0.2224,[72144e]|0.2258,0.2258,[72144e]|0.2399,0.2399,[72144e]|0.1731,0.1731,[72144e]|0.1184,0.1184,[72144e]|0.1611,0.1611,[72144e]|0.1611,0.1611,[72144e]|0.2292,0.2292,[72144e]|0.1643,0.1643,[72144e]|0.2292,0.2292,[72144e]|0.2064,0.2064,[72144e]|0.3053,0.3053,[72144e]|0.3215,0.3215,[72144e]|0.4149,0.4149,[72144e]|0.4119,0.4119,[72144e]|0.3494,0.3494,[72144e]|0.2884,0.2884,[72144e]|0.3053,0.3053,[72144e]|0.4087,0.4087,[72144e]|0.433,0.433,[72144e]|0.4409,0.4409,[72144e]|0.4685,0.4685,[72144e]|0.5176,0.5176,[72144e]|0.5139,0.5139,[72144e]|0.5296,0.5296,[72144e]|0.5098,0.5098,[72144e]|0.5098,0.5098,[72144e]|0.433,0.433,[72144e]|0.4369,0.4369,[72144e]|0.3249,0.3249,[72144e]|0.3249,0.3249,[72144e]|0.2951,0.2951,[72144e]|0.1969,0.1969,[72144e]|0.2064,0.2064,[72144e]|0.2002,0.2002,[72144e]|0.1942,0.1942,[72144e]|0.2094,0.2094,[72144e]|0.2436,0.2436,[72144e]|0.3087,0.3087,[72144e]|0.2258,0.2258,[72144e]|0.2328,0.2328,[72144e]|0.2164,0.2164,[72144e]|0.2034,0.2034,[72144e]|0.2541,0.2541,[72144e]|0.2575,0.2575,[72144e]|0.2783,0.2783,[72144e]|0.3019,0.3019,[72144e]|0.3019,0.3019,[72144e]|0.3529,0.3529,[72144e]|0.3948,0.3948,[72144e]|0.384,0.384,[72144e]|0.4766,0.4766,[72144e]|0.5254,0.5254,[72144e]|0.5419,0.5419,[72144e]|0.6755,0.6755,[72144e]|0.6136,0.6136,[72144e]|0.5901,0.5901,[72144e]|0.5807,0.5807,[72144e]|0.5382,0.5382,[72144e]|0.6322,0.6322,[72144e]|0.6089,0.6089,[72144e]|
+LINE_GRAPH     IUPredWS (Short)        <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.892,0.892,[329440]|0.835,0.835,[329440]|0.7388,0.7388,[329440]|0.6944,0.6944,[329440]|0.6557,0.6557,[329440]|0.6124,0.6124,[329440]|0.4967,0.4967,[329440]|0.4149,0.4149,[329440]|0.3939,0.3939,[329440]|0.3717,0.3717,[329440]|0.3359,0.3359,[329440]|0.3939,0.3939,[329440]|0.363,0.363,[329440]|0.3847,0.3847,[329440]|0.3535,0.3535,[329440]|0.3311,0.3311,[329440]|0.3053,0.3053,[329440]|0.3225,0.3225,[329440]|0.3992,0.3992,[329440]|0.3939,0.3939,[329440]|0.3939,0.3939,[329440]|0.4203,0.4203,[329440]|0.4781,0.4781,[329440]|0.4825,0.4825,[329440]|0.4513,0.4513,[329440]|0.363,0.363,[329440]|0.4651,0.4651,[329440]|0.4967,0.4967,[329440]|0.4749,0.4749,[329440]|0.3535,0.3535,[329440]|0.3456,0.3456,[329440]|0.2558,0.2558,[329440]|0.3225,0.3225,[329440]|0.2963,0.2963,[329440]|0.2602,0.2602,[329440]|0.2657,0.2657,[329440]|0.3184,0.3184,[329440]|0.3359,0.3359,[329440]|0.3491,0.3491,[329440]|0.3491,0.3491,[329440]|0.3578,0.3578,[329440]|0.3096,0.3096,[329440]|0.2865,0.2865,[329440]|0.2292,0.2292,[329440]|0.2292,0.2292,[329440]|0.2865,0.2865,[329440]|0.2292,0.2292,[329440]|0.2255,0.2255,[329440]|0.1566,0.1566,[329440]|0.2333,0.2333,[329440]|0.1766,0.1766,[329440]|0.2209,0.2209,[329440]|0.1602,0.1602,[329440]|0.1088,0.1088,[329440]|0.1495,0.1495,[329440]|0.1766,0.1766,[329440]|0.1921,0.1921,[329440]|0.1998,0.1998,[329440]|0.2122,0.2122,[329440]|0.2255,0.2255,[329440]|0.2385,0.2385,[329440]|0.2041,0.2041,[329440]|0.2483,0.2483,[329440]|0.2122,0.2122,[329440]|0.27,0.27,[329440]|0.3225,0.3225,[329440]|0.3762,0.3762,[329440]|0.3225,0.3225,[329440]|0.3311,0.3311,[329440]|0.2865,0.2865,[329440]|0.282,0.282,[329440]|0.3184,0.3184,[329440]|0.3668,0.3668,[329440]|0.4037,0.4037,[329440]|0.4245,0.4245,[329440]|0.4116,0.4116,[329440]|0.3359,0.3359,[329440]|0.3311,0.3311,[329440]|0.2483,0.2483,[329440]|0.2558,0.2558,[329440]|0.1766,0.1766,[329440]|0.2913,0.2913,[329440]|0.2041,0.2041,[329440]|0.3005,0.3005,[329440]|0.1416,0.1416,[329440]|0.1205,0.1205,[329440]|0.0884,0.0884,[329440]|0.1205,0.1205,[329440]|0.1766,0.1766,[329440]|0.1266,0.1266,[329440]|0.1766,0.1766,[329440]|0.1667,0.1667,[329440]|0.0991,0.0991,[329440]|0.1041,0.1041,[329440]|0.0935,0.0935,[329440]|0.0723,0.0723,[329440]|0.0771,0.0771,[329440]|0.0554,0.0554,[329440]|0.0771,0.0771,[329440]|0.066,0.066,[329440]|0.0935,0.0935,[329440]|0.0526,0.0526,[329440]|0.0771,0.0771,[329440]|0.0744,0.0744,[329440]|0.1805,0.1805,[329440]|0.2041,0.2041,[329440]|0.2333,0.2333,[329440]|0.2385,0.2385,[329440]|0.1667,0.1667,[329440]|0.2167,0.2167,[329440]|0.2255,0.2255,[329440]|0.2333,0.2333,[329440]|0.3717,0.3717,[329440]|0.4037,0.4037,[329440]|0.3399,0.3399,[329440]|0.3806,0.3806,[329440]|0.4333,0.4333,[329440]|0.4918,0.4918,[329440]|0.442,0.442,[329440]|0.3992,0.3992,[329440]|0.3399,0.3399,[329440]|0.4037,0.4037,[329440]|0.3456,0.3456,[329440]|0.2963,0.2963,[329440]|0.2602,0.2602,[329440]|0.1805,0.1805,[329440]|0.2209,0.2209,[329440]|0.2167,0.2167,[329440]|0.2963,0.2963,[329440]|0.3717,0.3717,[329440]|0.2913,0.2913,[329440]|0.2786,0.2786,[329440]|0.1921,0.1921,[329440]|0.2122,0.2122,[329440]|0.27,0.27,[329440]|0.2292,0.2292,[329440]|0.1998,0.1998,[329440]|0.2209,0.2209,[329440]|0.2963,0.2963,[329440]|0.3717,0.3717,[329440]|0.363,0.363,[329440]|0.3578,0.3578,[329440]|0.3992,0.3992,[329440]|0.4967,0.4967,[329440]|0.5549,0.5549,[329440]|0.665,0.665,[329440]|0.6681,0.6681,[329440]|0.7111,0.7111,[329440]|0.7501,0.7501,[329440]|0.7772,0.7772,[329440]|0.8677,0.8677,[329440]|0.904,0.904,[329440]|
+
+SEQUENCE_REF   FER1_PEA
+LINE_GRAPH     IUPredWS (Long) <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.1914,0.1914,[72144e]|0.2258,0.2258,[72144e]|0.268,0.268,[72144e]|0.2951,0.2951,[72144e]|0.1914,0.1914,[72144e]|0.1476,0.1476,[72144e]|0.1823,0.1823,[72144e]|0.2094,0.2094,[72144e]|0.247,0.247,[72144e]|0.3019,0.3019,[72144e]|0.2918,0.2918,[72144e]|0.3566,0.3566,[72144e]|0.3566,0.3566,[72144e]|0.3529,0.3529,[72144e]|0.2988,0.2988,[72144e]|0.2752,0.2752,[72144e]|0.3087,0.3087,[72144e]|0.3774,0.3774,[72144e]|0.4541,0.4541,[72144e]|0.4256,0.4256,[72144e]|0.3215,0.3215,[72144e]|0.346,0.346,[72144e]|0.4087,0.4087,[72144e]|0.4087,0.4087,[72144e]|0.3087,0.3087,[72144e]|0.2436,0.2436,[72144e]|0.3392,0.3392,[72144e]|0.3321,0.3321,[72144e]|0.3182,0.3182,[72144e]|0.3182,0.3182,[72144e]|0.3053,0.3053,[72144e]|0.2064,0.2064,[72144e]|0.2258,0.2258,[72144e]|0.1969,0.1969,[72144e]|0.2258,0.2258,[72144e]|0.2399,0.2399,[72144e]|0.2292,0.2292,[72144e]|0.2002,0.2002,[72144e]|0.1501,0.1501,[72144e]|0.1275,0.1275,[72144e]|0.1162,0.1162,[72144e]|0.1162,0.1162,[72144e]|0.1942,0.1942,[72144e]|0.1298,0.1298,[72144e]|0.1162,0.1162,[72144e]|0.0851,0.0851,[72144e]|0.1424,0.1424,[72144e]|0.1424,0.1424,[72144e]|0.1048,0.1048,[72144e]|0.1554,0.1554,[72144e]|0.1914,0.1914,[72144e]|0.2002,0.2002,[72144e]|0.2034,0.2034,[72144e]|0.2752,0.2752,[72144e]|0.2918,0.2918,[72144e]|0.3117,0.3117,[72144e]|0.2164,0.2164,[72144e]|0.2258,0.2258,[72144e]|0.2002,0.2002,[72144e]|0.2575,0.2575,[72144e]|0.3087,0.3087,[72144e]|0.3494,0.3494,[72144e]|0.3249,0.3249,[72144e]|0.2752,0.2752,[72144e]|0.2064,0.2064,[72144e]|0.2193,0.2193,[72144e]|0.247,0.247,[72144e]|0.2988,0.2988,[72144e]|0.2817,0.2817,[72144e]|0.3704,0.3704,[72144e]|0.4476,0.4476,[72144e]|0.391,0.391,[72144e]|0.3599,0.3599,[72144e]|0.2752,0.2752,[72144e]|0.2884,0.2884,[72144e]|0.2164,0.2164,[72144e]|0.2399,0.2399,[72144e]|0.1476,0.1476,[72144e]|0.2328,0.2328,[72144e]|0.1323,0.1323,[72144e]|0.2129,0.2129,[72144e]|0.1583,0.1583,[72144e]|0.1611,0.1611,[72144e]|0.1476,0.1476,[72144e]|0.1206,0.1206,[72144e]|0.1791,0.1791,[72144e]|0.2436,0.2436,[72144e]|0.2164,0.2164,[72144e]|0.1791,0.1791,[72144e]|0.1823,0.1823,[72144e]|0.1969,0.1969,[72144e]|0.1349,0.1349,[72144e]|0.0851,0.0851,[72144e]|0.1184,0.1184,[72144e]|0.1162,0.1162,[72144e]|0.1914,0.1914,[72144e]|0.1373,0.1373,[72144e]|0.2034,0.2034,[72144e]|0.1823,0.1823,[72144e]|0.2575,0.2575,[72144e]|0.2715,0.2715,[72144e]|0.3631,0.3631,[72144e]|0.3599,0.3599,[72144e]|0.2918,0.2918,[72144e]|0.2258,0.2258,[72144e]|0.2436,0.2436,[72144e]|0.3494,0.3494,[72144e]|0.374,0.374,[72144e]|0.384,0.384,[72144e]|0.4051,0.4051,[72144e]|0.4541,0.4541,[72144e]|0.4256,0.4256,[72144e]|0.4369,0.4369,[72144e]|0.391,0.391,[72144e]|0.3948,0.3948,[72144e]|0.3249,0.3249,[72144e]|0.3286,0.3286,[72144e]|0.2064,0.2064,[72144e]|0.2034,0.2034,[72144e]|0.1702,0.1702,[72144e]|0.1092,0.1092,[72144e]|0.1323,0.1323,[72144e]|0.1251,0.1251,[72144e]|0.1251,0.1251,[72144e]|0.1373,0.1373,[72144e]|0.1702,0.1702,[72144e]|0.1852,0.1852,[72144e]|0.1184,0.1184,[72144e]|0.1251,0.1251,[72144e]|0.1115,0.1115,[72144e]|0.1028,0.1028,[72144e]|0.1424,0.1424,[72144e]|0.1449,0.1449,[72144e]|0.1881,0.1881,[72144e]|0.2064,0.2064,[72144e]|0.2328,0.2328,[72144e]|0.2849,0.2849,[72144e]|0.3249,0.3249,[72144e]|0.3182,0.3182,[72144e]|0.4051,0.4051,[72144e]|0.4541,0.4541,[72144e]|0.4725,0.4725,[72144e]|0.5577,0.5577,[72144e]|0.494,0.494,[72144e]|0.4766,0.4766,[72144e]|0.4619,0.4619,[72144e]|0.4149,0.4149,[72144e]|0.4831,0.4831,[72144e]|0.5665,0.5665,[72144e]|
+LINE_GRAPH     IUPredWS (Short)        <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.8781,0.8781,[329440]|0.82,0.82,[329440]|0.7192,0.7192,[329440]|0.6756,0.6756,[329440]|0.6374,0.6374,[329440]|0.59,0.59,[329440]|0.4651,0.4651,[329440]|0.3578,0.3578,[329440]|0.3359,0.3359,[329440]|0.2913,0.2913,[329440]|0.2531,0.2531,[329440]|0.3184,0.3184,[329440]|0.3184,0.3184,[329440]|0.3491,0.3491,[329440]|0.3184,0.3184,[329440]|0.2913,0.2913,[329440]|0.2531,0.2531,[329440]|0.2963,0.2963,[329440]|0.3806,0.3806,[329440]|0.3762,0.3762,[329440]|0.3806,0.3806,[329440]|0.3717,0.3717,[329440]|0.3399,0.3399,[329440]|0.3456,0.3456,[329440]|0.3535,0.3535,[329440]|0.3535,0.3535,[329440]|0.3359,0.3359,[329440]|0.3263,0.3263,[329440]|0.3053,0.3053,[329440]|0.2333,0.2333,[329440]|0.2255,0.2255,[329440]|0.1958,0.1958,[329440]|0.2292,0.2292,[329440]|0.1456,0.1456,[329440]|0.1698,0.1698,[329440]|0.1805,0.1805,[329440]|0.2385,0.2385,[329440]|0.2483,0.2483,[329440]|0.1878,0.1878,[329440]|0.1635,0.1635,[329440]|0.1178,0.1178,[329440]|0.1205,0.1205,[329440]|0.1667,0.1667,[329440]|0.138,0.138,[329440]|0.1322,0.1322,[329440]|0.0813,0.0813,[329440]|0.1416,0.1416,[329440]|0.1456,0.1456,[329440]|0.1349,0.1349,[329440]|0.1322,0.1322,[329440]|0.0909,0.0909,[329440]|0.0884,0.0884,[329440]|0.1088,0.1088,[329440]|0.1602,0.1602,[329440]|0.1635,0.1635,[329440]|0.1495,0.1495,[329440]|0.1635,0.1635,[329440]|0.1698,0.1698,[329440]|0.1456,0.1456,[329440]|0.1844,0.1844,[329440]|0.1602,0.1602,[329440]|0.2167,0.2167,[329440]|0.2483,0.2483,[329440]|0.3053,0.3053,[329440]|0.2483,0.2483,[329440]|0.2602,0.2602,[329440]|0.2122,0.2122,[329440]|0.2167,0.2167,[329440]|0.2432,0.2432,[329440]|0.3053,0.3053,[329440]|0.3263,0.3263,[329440]|0.3491,0.3491,[329440]|0.3359,0.3359,[329440]|0.2748,0.2748,[329440]|0.27,0.27,[329440]|0.2209,0.2209,[329440]|0.2292,0.2292,[329440]|0.1602,0.1602,[329440]|0.2748,0.2748,[329440]|0.1921,0.1921,[329440]|0.282,0.282,[329440]|0.1322,0.1322,[329440]|0.124,0.124,[329440]|0.0909,0.0909,[329440]|0.124,0.124,[329440]|0.1805,0.1805,[329440]|0.1322,0.1322,[329440]|0.1844,0.1844,[329440]|0.1732,0.1732,[329440]|0.1041,0.1041,[329440]|0.1088,0.1088,[329440]|0.0991,0.0991,[329440]|0.0771,0.0771,[329440]|0.0771,0.0771,[329440]|0.0554,0.0554,[329440]|0.0771,0.0771,[329440]|0.0643,0.0643,[329440]|0.1088,0.1088,[329440]|0.0607,0.0607,[329440]|0.1041,0.1041,[329440]|0.1041,0.1041,[329440]|0.208,0.208,[329440]|0.2385,0.2385,[329440]|0.2657,0.2657,[329440]|0.2748,0.2748,[329440]|0.1878,0.1878,[329440]|0.2292,0.2292,[329440]|0.2483,0.2483,[329440]|0.2602,0.2602,[329440]|0.3992,0.3992,[329440]|0.4282,0.4282,[329440]|0.363,0.363,[329440]|0.4116,0.4116,[329440]|0.4333,0.4333,[329440]|0.4967,0.4967,[329440]|0.4203,0.4203,[329440]|0.3762,0.3762,[329440]|0.282,0.282,[329440]|0.3399,0.3399,[329440]|0.2558,0.2558,[329440]|0.1998,0.1998,[329440]|0.1844,0.1844,[329440]|0.1178,0.1178,[329440]|0.1566,0.1566,[329440]|0.1495,0.1495,[329440]|0.2209,0.2209,[329440]|0.3053,0.3053,[329440]|0.2209,0.2209,[329440]|0.1566,0.1566,[329440]|0.0884,0.0884,[329440]|0.1041,0.1041,[329440]|0.1416,0.1416,[329440]|0.1178,0.1178,[329440]|0.1205,0.1205,[329440]|0.1349,0.1349,[329440]|0.2209,0.2209,[329440]|0.282,0.282,[329440]|0.2748,0.2748,[329440]|0.27,0.27,[329440]|0.3005,0.3005,[329440]|0.3992,0.3992,[329440]|0.4703,0.4703,[329440]|0.5762,0.5762,[329440]|0.5762,0.5762,[329440]|0.6293,0.6293,[329440]|0.6715,0.6715,[329440]|0.6944,0.6944,[329440]|0.7951,0.7951,[329440]|0.8781,0.8781,[329440]|
+
+SEQUENCE_REF   FER1_SPIOL
+LINE_GRAPH     IUPredWS (Long) <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.3704,0.3704,[72144e]|0.4017,0.4017,[72144e]|0.4292,0.4292,[72144e]|0.3215,0.3215,[72144e]|0.2884,0.2884,[72144e]|0.3566,0.3566,[72144e]|0.3704,0.3704,[72144e]|0.4292,0.4292,[72144e]|0.4619,0.4619,[72144e]|0.4476,0.4476,[72144e]|0.4979,0.4979,[72144e]|0.5807,0.5807,[72144e]|0.5758,0.5758,[72144e]|0.5758,0.5758,[72144e]|0.5382,0.5382,[72144e]|0.5055,0.5055,[72144e]|0.4409,0.4409,[72144e]|0.4685,0.4685,[72144e]|0.5055,0.5055,[72144e]|0.5493,0.5493,[72144e]|0.5533,0.5533,[72144e]|0.5951,0.5951,[72144e]|0.6375,0.6375,[72144e]|0.6322,0.6322,[72144e]|0.5493,0.5493,[72144e]|0.5456,0.5456,[72144e]|0.6043,0.6043,[72144e]|0.4864,0.4864,[72144e]|0.4864,0.4864,[72144e]|0.4507,0.4507,[72144e]|0.4369,0.4369,[72144e]|0.4652,0.4652,[72144e]|0.433,0.433,[72144e]|0.3983,0.3983,[72144e]|0.4292,0.4292,[72144e]|0.4619,0.4619,[72144e]|0.4541,0.4541,[72144e]|0.4831,0.4831,[72144e]|0.5176,0.5176,[72144e]|0.4541,0.4541,[72144e]|0.433,0.433,[72144e]|0.3392,0.3392,[72144e]|0.3286,0.3286,[72144e]|0.2849,0.2849,[72144e]|0.2817,0.2817,[72144e]|0.2224,0.2224,[72144e]|0.2364,0.2364,[72144e]|0.3249,0.3249,[72144e]|0.3599,0.3599,[72144e]|0.422,0.422,[72144e]|0.433,0.433,[72144e]|0.4409,0.4409,[72144e]|0.391,0.391,[72144e]|0.4186,0.4186,[72144e]|0.3249,0.3249,[72144e]|0.3392,0.3392,[72144e]|0.247,0.247,[72144e]|0.2783,0.2783,[72144e]|0.3215,0.3215,[72144e]|0.3321,0.3321,[72144e]|0.3182,0.3182,[72144e]|0.2609,0.2609,[72144e]|0.2193,0.2193,[72144e]|0.247,0.247,[72144e]|0.268,0.268,[72144e]|0.2918,0.2918,[72144e]|0.2645,0.2645,[72144e]|0.3494,0.3494,[72144e]|0.422,0.422,[72144e]|0.4476,0.4476,[72144e]|0.4119,0.4119,[72144e]|0.346,0.346,[72144e]|0.3599,0.3599,[72144e]|0.2918,0.2918,[72144e]|0.3704,0.3704,[72144e]|0.2609,0.2609,[72144e]|0.3494,0.3494,[72144e]|0.2436,0.2436,[72144e]|0.3392,0.3392,[72144e]|0.2817,0.2817,[72144e]|0.268,0.268,[72144e]|0.2541,0.2541,[72144e]|0.2094,0.2094,[72144e]|0.2951,0.2951,[72144e]|0.3566,0.3566,[72144e]|0.3215,0.3215,[72144e]|0.2849,0.2849,[72144e]|0.3117,0.3117,[72144e]|0.3249,0.3249,[72144e]|0.2399,0.2399,[72144e]|0.2064,0.2064,[72144e]|0.1852,0.1852,[72144e]|0.1852,0.1852,[72144e]|0.247,0.247,[72144e]|0.1759,0.1759,[72144e]|0.2399,0.2399,[72144e]|0.2193,0.2193,[72144e]|0.3182,0.3182,[72144e]|0.3321,0.3321,[72144e]|0.4369,0.4369,[72144e]|0.433,0.433,[72144e]|0.3704,0.3704,[72144e]|0.3087,0.3087,[72144e]|0.3249,0.3249,[72144e]|0.433,0.433,[72144e]|0.4476,0.4476,[72144e]|0.4582,0.4582,[72144e]|0.4864,0.4864,[72144e]|0.5296,0.5296,[72144e]|0.5533,0.5533,[72144e]|0.5665,0.5665,[72144e]|0.5456,0.5456,[72144e]|0.5017,0.5017,[72144e]|0.4369,0.4369,[72144e]|0.4369,0.4369,[72144e]|0.3356,0.3356,[72144e]|0.374,0.374,[72144e]|0.3426,0.3426,[72144e]|0.2609,0.2609,[72144e]|0.2817,0.2817,[72144e]|0.2164,0.2164,[72144e]|0.2034,0.2034,[72144e]|0.2164,0.2164,[72144e]|0.2541,0.2541,[72144e]|0.3117,0.3117,[72144e]|0.2328,0.2328,[72144e]|0.2399,0.2399,[72144e]|0.2224,0.2224,[72144e]|0.2064,0.2064,[72144e]|0.2575,0.2575,[72144e]|0.268,0.268,[72144e]|0.268,0.268,[72144e]|0.2918,0.2918,[72144e]|0.3019,0.3019,[72144e]|0.3494,0.3494,[72144e]|0.3872,0.3872,[72144e]|0.3807,0.3807,[72144e]|0.4685,0.4685,[72144e]|0.4831,0.4831,[72144e]|0.494,0.494,[72144e]|0.5854,0.5854,[72144e]|0.5176,0.5176,[72144e]|0.5807,0.5807,[72144e]|0.5707,0.5707,[72144e]|0.5296,0.5296,[72144e]|0.6183,0.6183,[72144e]|0.5992,0.5992,[72144e]|
+LINE_GRAPH     IUPredWS (Short)        <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.928,0.928,[329440]|0.8823,0.8823,[329440]|0.8283,0.8283,[329440]|0.7912,0.7912,[329440]|0.754,0.754,[329440]|0.6474,0.6474,[329440]|0.5473,0.5473,[329440]|0.5296,0.5296,[329440]|0.4918,0.4918,[329440]|0.4703,0.4703,[329440]|0.4379,0.4379,[329440]|0.442,0.442,[329440]|0.4967,0.4967,[329440]|0.5514,0.5514,[329440]|0.5229,0.5229,[329440]|0.4879,0.4879,[329440]|0.4556,0.4556,[329440]|0.4245,0.4245,[329440]|0.4116,0.4116,[329440]|0.4651,0.4651,[329440]|0.4703,0.4703,[329440]|0.5008,0.5008,[329440]|0.5296,0.5296,[329440]|0.5229,0.5229,[329440]|0.5374,0.5374,[329440]|0.6174,0.6174,[329440]|0.6255,0.6255,[329440]|0.5253,0.5253,[329440]|0.5229,0.5229,[329440]|0.4458,0.4458,[329440]|0.442,0.442,[329440]|0.4781,0.4781,[329440]|0.4513,0.4513,[329440]|0.4282,0.4282,[329440]|0.4749,0.4749,[329440]|0.4967,0.4967,[329440]|0.5173,0.5173,[329440]|0.5549,0.5549,[329440]|0.5667,0.5667,[329440]|0.5412,0.5412,[329440]|0.5043,0.5043,[329440]|0.4703,0.4703,[329440]|0.4333,0.4333,[329440]|0.3578,0.3578,[329440]|0.3311,0.3311,[329440]|0.2657,0.2657,[329440]|0.3146,0.3146,[329440]|0.3263,0.3263,[329440]|0.27,0.27,[329440]|0.3184,0.3184,[329440]|0.3456,0.3456,[329440]|0.3311,0.3311,[329440]|0.3311,0.3311,[329440]|0.3311,0.3311,[329440]|0.2531,0.2531,[329440]|0.2748,0.2748,[329440]|0.1921,0.1921,[329440]|0.1921,0.1921,[329440]|0.1456,0.1456,[329440]|0.1698,0.1698,[329440]|0.2122,0.2122,[329440]|0.2657,0.2657,[329440]|0.2333,0.2333,[329440]|0.2385,0.2385,[329440]|0.1844,0.1844,[329440]|0.1844,0.1844,[329440]|0.1998,0.1998,[329440]|0.2209,0.2209,[329440]|0.2432,0.2432,[329440]|0.2657,0.2657,[329440]|0.2483,0.2483,[329440]|0.27,0.27,[329440]|0.2657,0.2657,[329440]|0.208,0.208,[329440]|0.282,0.282,[329440]|0.1998,0.1998,[329440]|0.3184,0.3184,[329440]|0.2432,0.2432,[329440]|0.3359,0.3359,[329440]|0.1732,0.1732,[329440]|0.1566,0.1566,[329440]|0.1205,0.1205,[329440]|0.1602,0.1602,[329440]|0.2255,0.2255,[329440]|0.1766,0.1766,[329440]|0.2385,0.2385,[329440]|0.2255,0.2255,[329440]|0.1635,0.1635,[329440]|0.1732,0.1732,[329440]|0.1602,0.1602,[329440]|0.1292,0.1292,[329440]|0.0771,0.0771,[329440]|0.0701,0.0701,[329440]|0.0965,0.0965,[329440]|0.0858,0.0858,[329440]|0.124,0.124,[329440]|0.0643,0.0643,[329440]|0.0935,0.0935,[329440]|0.0935,0.0935,[329440]|0.2041,0.2041,[329440]|0.2209,0.2209,[329440]|0.2602,0.2602,[329440]|0.2657,0.2657,[329440]|0.1878,0.1878,[329440]|0.2333,0.2333,[329440]|0.2432,0.2432,[329440]|0.2531,0.2531,[329440]|0.3668,0.3668,[329440]|0.3992,0.3992,[329440]|0.3359,0.3359,[329440]|0.3717,0.3717,[329440]|0.4556,0.4556,[329440]|0.4825,0.4825,[329440]|0.4245,0.4245,[329440]|0.3806,0.3806,[329440]|0.3146,0.3146,[329440]|0.3762,0.3762,[329440]|0.3263,0.3263,[329440]|0.3005,0.3005,[329440]|0.2748,0.2748,[329440]|0.1998,0.1998,[329440]|0.2432,0.2432,[329440]|0.1878,0.1878,[329440]|0.2657,0.2657,[329440]|0.3456,0.3456,[329440]|0.2748,0.2748,[329440]|0.2558,0.2558,[329440]|0.1766,0.1766,[329440]|0.1998,0.1998,[329440]|0.2483,0.2483,[329440]|0.2209,0.2209,[329440]|0.1732,0.1732,[329440]|0.1921,0.1921,[329440]|0.282,0.282,[329440]|0.3535,0.3535,[329440]|0.3456,0.3456,[329440]|0.3491,0.3491,[329440]|0.3806,0.3806,[329440]|0.4458,0.4458,[329440]|0.5084,0.5084,[329440]|0.6174,0.6174,[329440]|0.6174,0.6174,[329440]|0.7034,0.7034,[329440]|0.7418,0.7418,[329440]|0.7644,0.7644,[329440]|0.8595,0.8595,[329440]|0.8945,0.8945,[329440]|
+
+SEQUENCE_REF   FER1_MESCR
+LINE_GRAPH     IUPredWS (Long) <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.3117,0.3117,[72144e]|0.2951,0.2951,[72144e]|0.3249,0.3249,[72144e]|0.3566,0.3566,[72144e]|0.3426,0.3426,[72144e]|0.2503,0.2503,[72144e]|0.2436,0.2436,[72144e]|0.3053,0.3053,[72144e]|0.3182,0.3182,[72144e]|0.3426,0.3426,[72144e]|0.3948,0.3948,[72144e]|0.4619,0.4619,[72144e]|0.4619,0.4619,[72144e]|0.4979,0.4979,[72144e]|0.4652,0.4652,[72144e]|0.433,0.433,[72144e]|0.3983,0.3983,[72144e]|0.4619,0.4619,[72144e]|0.5296,0.5296,[72144e]|0.5419,0.5419,[72144e]|0.4864,0.4864,[72144e]|0.5176,0.5176,[72144e]|0.5176,0.5176,[72144e]|0.5176,0.5176,[72144e]|0.4541,0.4541,[72144e]|0.3599,0.3599,[72144e]|0.3872,0.3872,[72144e]|0.4119,0.4119,[72144e]|0.4292,0.4292,[72144e]|0.3948,0.3948,[72144e]|0.4017,0.4017,[72144e]|0.3704,0.3704,[72144e]|0.3356,0.3356,[72144e]|0.3053,0.3053,[72144e]|0.3286,0.3286,[72144e]|0.3286,0.3286,[72144e]|0.3087,0.3087,[72144e]|0.3392,0.3392,[72144e]|0.3774,0.3774,[72144e]|0.3182,0.3182,[72144e]|0.2918,0.2918,[72144e]|0.2609,0.2609,[72144e]|0.2292,0.2292,[72144e]|0.2224,0.2224,[72144e]|0.1731,0.1731,[72144e]|0.2002,0.2002,[72144e]|0.2002,0.2002,[72144e]|0.2436,0.2436,[72144e]|0.247,0.247,[72144e]|0.3426,0.3426,[72144e]|0.3774,0.3774,[72144e]|0.3774,0.3774,[72144e]|0.3704,0.3704,[72144e]|0.4087,0.4087,[72144e]|0.4369,0.4369,[72144e]|0.3704,0.3704,[72144e]|0.3948,0.3948,[72144e]|0.2988,0.2988,[72144e]|0.3807,0.3807,[72144e]|0.391,0.391,[72144e]|0.4292,0.4292,[72144e]|0.4087,0.4087,[72144e]|0.3529,0.3529,[72144e]|0.3149,0.3149,[72144e]|0.3356,0.3356,[72144e]|0.3566,0.3566,[72144e]|0.3807,0.3807,[72144e]|0.3529,0.3529,[72144e]|0.4369,0.4369,[72144e]|0.5139,0.5139,[72144e]|0.4831,0.4831,[72144e]|0.4507,0.4507,[72144e]|0.3566,0.3566,[72144e]|0.3704,0.3704,[72144e]|0.3182,0.3182,[72144e]|0.3392,0.3392,[72144e]|0.2328,0.2328,[72144e]|0.2951,0.2951,[72144e]|0.1791,0.1791,[72144e]|0.2715,0.2715,[72144e]|0.2164,0.2164,[72144e]|0.2002,0.2002,[72144e]|0.1881,0.1881,[72144e]|0.1501,0.1501,[72144e]|0.2164,0.2164,[72144e]|0.2817,0.2817,[72144e]|0.247,0.247,[72144e]|0.2094,0.2094,[72144e]|0.2328,0.2328,[72144e]|0.2503,0.2503,[72144e]|0.1823,0.1823,[72144e]|0.1643,0.1643,[72144e]|0.1852,0.1852,[72144e]|0.1852,0.1852,[72144e]|0.247,0.247,[72144e]|0.1881,0.1881,[72144e]|0.2541,0.2541,[72144e]|0.2328,0.2328,[72144e]|0.3249,0.3249,[72144e]|0.3426,0.3426,[72144e]|0.4369,0.4369,[72144e]|0.4292,0.4292,[72144e]|0.3704,0.3704,[72144e]|0.3117,0.3117,[72144e]|0.3249,0.3249,[72144e]|0.4369,0.4369,[72144e]|0.4507,0.4507,[72144e]|0.4619,0.4619,[72144e]|0.4901,0.4901,[72144e]|0.5055,0.5055,[72144e]|0.5342,0.5342,[72144e]|0.5419,0.5419,[72144e]|0.5176,0.5176,[72144e]|0.4619,0.4619,[72144e]|0.4017,0.4017,[72144e]|0.4051,0.4051,[72144e]|0.3053,0.3053,[72144e]|0.3053,0.3053,[72144e]|0.2783,0.2783,[72144e]|0.1942,0.1942,[72144e]|0.2129,0.2129,[72144e]|0.2002,0.2002,[72144e]|0.2002,0.2002,[72144e]|0.2129,0.2129,[72144e]|0.2503,0.2503,[72144e]|0.3117,0.3117,[72144e]|0.2328,0.2328,[72144e]|0.2399,0.2399,[72144e]|0.2258,0.2258,[72144e]|0.2129,0.2129,[72144e]|0.268,0.268,[72144e]|0.2988,0.2988,[72144e]|0.2988,0.2988,[72144e]|0.3215,0.3215,[72144e]|0.3249,0.3249,[72144e]|0.3774,0.3774,[72144e]|0.4149,0.4149,[72144e]|0.4051,0.4051,[72144e]|0.4979,0.4979,[72144e]|0.5456,0.5456,[72144e]|0.5665,0.5665,[72144e]|0.6755,0.6755,[72144e]|0.6089,0.6089,[72144e]|0.5901,0.5901,[72144e]|0.5807,0.5807,[72144e]|0.5382,0.5382,[72144e]|0.6227,0.6227,[72144e]|0.6043,0.6043,[72144e]|
+LINE_GRAPH     IUPredWS (Short)        <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.8857,0.8857,[329440]|0.8283,0.8283,[329440]|0.7912,0.7912,[329440]|0.7111,0.7111,[329440]|0.6681,0.6681,[329440]|0.6334,0.6334,[329440]|0.5549,0.5549,[329440]|0.4282,0.4282,[329440]|0.3491,0.3491,[329440]|0.3311,0.3311,[329440]|0.2913,0.2913,[329440]|0.3225,0.3225,[329440]|0.3806,0.3806,[329440]|0.442,0.442,[329440]|0.4078,0.4078,[329440]|0.4078,0.4078,[329440]|0.4078,0.4078,[329440]|0.4037,0.4037,[329440]|0.3939,0.3939,[329440]|0.4203,0.4203,[329440]|0.4245,0.4245,[329440]|0.46,0.46,[329440]|0.3885,0.3885,[329440]|0.4282,0.4282,[329440]|0.4556,0.4556,[329440]|0.4149,0.4149,[329440]|0.3885,0.3885,[329440]|0.3847,0.3847,[329440]|0.4203,0.4203,[329440]|0.3263,0.3263,[329440]|0.3311,0.3311,[329440]|0.3263,0.3263,[329440]|0.3005,0.3005,[329440]|0.2432,0.2432,[329440]|0.2786,0.2786,[329440]|0.2865,0.2865,[329440]|0.3146,0.3146,[329440]|0.3578,0.3578,[329440]|0.3535,0.3535,[329440]|0.3263,0.3263,[329440]|0.2913,0.2913,[329440]|0.2558,0.2558,[329440]|0.2913,0.2913,[329440]|0.2657,0.2657,[329440]|0.1698,0.1698,[329440]|0.1958,0.1958,[329440]|0.1878,0.1878,[329440]|0.2748,0.2748,[329440]|0.2041,0.2041,[329440]|0.208,0.208,[329440]|0.1998,0.1998,[329440]|0.2333,0.2333,[329440]|0.2483,0.2483,[329440]|0.2748,0.2748,[329440]|0.2602,0.2602,[329440]|0.2602,0.2602,[329440]|0.2786,0.2786,[329440]|0.1998,0.1998,[329440]|0.2748,0.2748,[329440]|0.1844,0.1844,[329440]|0.2483,0.2483,[329440]|0.2913,0.2913,[329440]|0.3456,0.3456,[329440]|0.3184,0.3184,[329440]|0.3225,0.3225,[329440]|0.27,0.27,[329440]|0.2748,0.2748,[329440]|0.2913,0.2913,[329440]|0.3225,0.3225,[329440]|0.3491,0.3491,[329440]|0.3717,0.3717,[329440]|0.3578,0.3578,[329440]|0.3053,0.3053,[329440]|0.3005,0.3005,[329440]|0.2602,0.2602,[329440]|0.2748,0.2748,[329440]|0.1958,0.1958,[329440]|0.3005,0.3005,[329440]|0.2209,0.2209,[329440]|0.3146,0.3146,[329440]|0.1602,0.1602,[329440]|0.138,0.138,[329440]|0.1041,0.1041,[329440]|0.1349,0.1349,[329440]|0.1958,0.1958,[329440]|0.1532,0.1532,[329440]|0.2041,0.2041,[329440]|0.1878,0.1878,[329440]|0.1322,0.1322,[329440]|0.1349,0.1349,[329440]|0.124,0.124,[329440]|0.0991,0.0991,[329440]|0.0884,0.0884,[329440]|0.0858,0.0858,[329440]|0.1205,0.1205,[329440]|0.1018,0.1018,[329440]|0.138,0.138,[329440]|0.0832,0.0832,[329440]|0.1178,0.1178,[329440]|0.1178,0.1178,[329440]|0.2385,0.2385,[329440]|0.2602,0.2602,[329440]|0.2865,0.2865,[329440]|0.2963,0.2963,[329440]|0.2209,0.2209,[329440]|0.2748,0.2748,[329440]|0.2865,0.2865,[329440]|0.2963,0.2963,[329440]|0.4116,0.4116,[329440]|0.442,0.442,[329440]|0.3885,0.3885,[329440]|0.3885,0.3885,[329440]|0.4651,0.4651,[329440]|0.4749,0.4749,[329440]|0.4149,0.4149,[329440]|0.3762,0.3762,[329440]|0.3184,0.3184,[329440]|0.3668,0.3668,[329440]|0.3146,0.3146,[329440]|0.2657,0.2657,[329440]|0.2333,0.2333,[329440]|0.1667,0.1667,[329440]|0.208,0.208,[329440]|0.1998,0.1998,[329440]|0.2786,0.2786,[329440]|0.3456,0.3456,[329440]|0.2786,0.2786,[329440]|0.2602,0.2602,[329440]|0.1844,0.1844,[329440]|0.1998,0.1998,[329440]|0.2483,0.2483,[329440]|0.2531,0.2531,[329440]|0.2041,0.2041,[329440]|0.2209,0.2209,[329440]|0.2963,0.2963,[329440]|0.3578,0.3578,[329440]|0.3491,0.3491,[329440]|0.3491,0.3491,[329440]|0.3847,0.3847,[329440]|0.4781,0.4781,[329440]|0.5374,0.5374,[329440]|0.6442,0.6442,[329440]|0.6474,0.6474,[329440]|0.6944,0.6944,[329440]|0.7317,0.7317,[329440]|0.7605,0.7605,[329440]|0.8521,0.8521,[329440]|0.892,0.892,[329440]|
+
+SEQUENCE_REF   FER_CAPAN
+LINE_GRAPH     IUPredWS (Long) <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.2817,0.2817,[72144e]|0.1671,0.1671,[72144e]|0.1611,0.1611,[72144e]|0.2364,0.2364,[72144e]|0.2783,0.2783,[72144e]|0.2951,0.2951,[72144e]|0.3566,0.3566,[72144e]|0.3426,0.3426,[72144e]|0.3053,0.3053,[72144e]|0.3286,0.3286,[72144e]|0.346,0.346,[72144e]|0.3087,0.3087,[72144e]|0.3321,0.3321,[72144e]|0.3631,0.3631,[72144e]|0.346,0.346,[72144e]|0.3774,0.3774,[72144e]|0.4119,0.4119,[72144e]|0.3566,0.3566,[72144e]|0.384,0.384,[72144e]|0.4766,0.4766,[72144e]|0.4507,0.4507,[72144e]|0.3807,0.3807,[72144e]|0.2884,0.2884,[72144e]|0.3774,0.3774,[72144e]|0.3392,0.3392,[72144e]|0.3019,0.3019,[72144e]|0.2918,0.2918,[72144e]|0.2752,0.2752,[72144e]|0.2503,0.2503,[72144e]|0.2752,0.2752,[72144e]|0.3249,0.3249,[72144e]|0.3149,0.3149,[72144e]|0.2645,0.2645,[72144e]|0.3356,0.3356,[72144e]|0.2399,0.2399,[72144e]|0.1852,0.1852,[72144e]|0.2258,0.2258,[72144e]|0.1969,0.1969,[72144e]|0.1251,0.1251,[72144e]|0.1583,0.1583,[72144e]|0.1229,0.1229,[72144e]|0.1028,0.1028,[72144e]|0.0817,0.0817,[72144e]|0.0799,0.0799,[72144e]|0.1399,0.1399,[72144e]|0.1611,0.1611,[72144e]|0.2399,0.2399,[72144e]|0.247,0.247,[72144e]|0.2783,0.2783,[72144e]|0.2328,0.2328,[72144e]|0.2503,0.2503,[72144e]|0.1643,0.1643,[72144e]|0.1791,0.1791,[72144e]|0.1092,0.1092,[72144e]|0.1702,0.1702,[72144e]|0.1791,0.1791,[72144e]|0.2849,0.2849,[72144e]|0.2645,0.2645,[72144e]|0.2094,0.2094,[72144e]|0.1501,0.1501,[72144e]|0.1643,0.1643,[72144e]|0.1852,0.1852,[72144e]|0.247,0.247,[72144e]|0.2258,0.2258,[72144e]|0.3149,0.3149,[72144e]|0.4087,0.4087,[72144e]|0.3774,0.3774,[72144e]|0.346,0.346,[72144e]|0.3286,0.3286,[72144e]|0.3494,0.3494,[72144e]|0.2541,0.2541,[72144e]|0.3529,0.3529,[72144e]|0.247,0.247,[72144e]|0.3392,0.3392,[72144e]|0.2224,0.2224,[72144e]|0.3249,0.3249,[72144e]|0.268,0.268,[72144e]|0.2541,0.2541,[72144e]|0.2436,0.2436,[72144e]|0.1969,0.1969,[72144e]|0.2752,0.2752,[72144e]|0.3426,0.3426,[72144e]|0.3053,0.3053,[72144e]|0.2645,0.2645,[72144e]|0.2503,0.2503,[72144e]|0.2715,0.2715,[72144e]|0.1823,0.1823,[72144e]|0.1424,0.1424,[72144e]|0.1611,0.1611,[72144e]|0.1611,0.1611,[72144e]|0.1424,0.1424,[72144e]|0.0967,0.0967,[72144e]|0.1528,0.1528,[72144e]|0.1399,0.1399,[72144e]|0.2129,0.2129,[72144e]|0.2292,0.2292,[72144e]|0.3286,0.3286,[72144e]|0.3356,0.3356,[72144e]|0.2752,0.2752,[72144e]|0.2094,0.2094,[72144e]|0.2292,0.2292,[72144e]|0.346,0.346,[72144e]|0.3631,0.3631,[72144e]|0.374,0.374,[72144e]|0.4119,0.4119,[72144e]|0.4619,0.4619,[72144e]|0.4864,0.4864,[72144e]|0.4901,0.4901,[72144e]|0.4979,0.4979,[72144e]|0.4725,0.4725,[72144e]|0.4051,0.4051,[72144e]|0.4087,0.4087,[72144e]|0.3182,0.3182,[72144e]|0.3215,0.3215,[72144e]|0.2817,0.2817,[72144e]|0.1969,0.1969,[72144e]|0.2224,0.2224,[72144e]|0.2164,0.2164,[72144e]|0.2129,0.2129,[72144e]|0.2193,0.2193,[72144e]|0.2575,0.2575,[72144e]|0.3215,0.3215,[72144e]|0.2399,0.2399,[72144e]|0.2436,0.2436,[72144e]|0.2292,0.2292,[72144e]|0.2164,0.2164,[72144e]|0.268,0.268,[72144e]|0.268,0.268,[72144e]|0.2193,0.2193,[72144e]|0.2436,0.2436,[72144e]|0.2436,0.2436,[72144e]|0.247,0.247,[72144e]|0.3087,0.3087,[72144e]|0.3019,0.3019,[72144e]|0.4017,0.4017,[72144e]|0.4441,0.4441,[72144e]|0.4541,0.4541,[72144e]|0.5419,0.5419,[72144e]|0.4831,0.4831,[72144e]|0.4507,0.4507,[72144e]|0.4369,0.4369,[72144e]|0.391,0.391,[72144e]|0.4541,0.4541,[72144e]|0.4292,0.4292,[72144e]|
+LINE_GRAPH     IUPredWS (Short)        <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.8424,0.8424,[329440]|0.8074,0.8074,[329440]|0.7644,0.7644,[329440]|0.6442,0.6442,[329440]|0.5762,0.5762,[329440]|0.5549,0.5549,[329440]|0.5253,0.5253,[329440]|0.4879,0.4879,[329440]|0.4651,0.4651,[329440]|0.3847,0.3847,[329440]|0.2748,0.2748,[329440]|0.2963,0.2963,[329440]|0.3311,0.3311,[329440]|0.2657,0.2657,[329440]|0.3311,0.3311,[329440]|0.3535,0.3535,[329440]|0.3146,0.3146,[329440]|0.3311,0.3311,[329440]|0.3578,0.3578,[329440]|0.363,0.363,[329440]|0.3578,0.3578,[329440]|0.363,0.363,[329440]|0.3225,0.3225,[329440]|0.3491,0.3491,[329440]|0.2913,0.2913,[329440]|0.2657,0.2657,[329440]|0.1878,0.1878,[329440]|0.1878,0.1878,[329440]|0.1732,0.1732,[329440]|0.1732,0.1732,[329440]|0.2292,0.2292,[329440]|0.2255,0.2255,[329440]|0.2255,0.2255,[329440]|0.282,0.282,[329440]|0.2209,0.2209,[329440]|0.1958,0.1958,[329440]|0.1844,0.1844,[329440]|0.138,0.138,[329440]|0.1088,0.1088,[329440]|0.1602,0.1602,[329440]|0.1041,0.1041,[329440]|0.0965,0.0965,[329440]|0.0813,0.0813,[329440]|0.1088,0.1088,[329440]|0.1205,0.1205,[329440]|0.0789,0.0789,[329440]|0.1117,0.1117,[329440]|0.1322,0.1322,[329440]|0.1349,0.1349,[329440]|0.1602,0.1602,[329440]|0.1805,0.1805,[329440]|0.1322,0.1322,[329440]|0.1495,0.1495,[329440]|0.0965,0.0965,[329440]|0.1495,0.1495,[329440]|0.0771,0.0771,[329440]|0.1495,0.1495,[329440]|0.1921,0.1921,[329440]|0.2209,0.2209,[329440]|0.1698,0.1698,[329440]|0.1805,0.1805,[329440]|0.1456,0.1456,[329440]|0.1495,0.1495,[329440]|0.1732,0.1732,[329440]|0.2432,0.2432,[329440]|0.2786,0.2786,[329440]|0.3053,0.3053,[329440]|0.2913,0.2913,[329440]|0.2432,0.2432,[329440]|0.2432,0.2432,[329440]|0.1958,0.1958,[329440]|0.2865,0.2865,[329440]|0.2041,0.2041,[329440]|0.3225,0.3225,[329440]|0.2385,0.2385,[329440]|0.3578,0.3578,[329440]|0.1844,0.1844,[329440]|0.1698,0.1698,[329440]|0.1495,0.1495,[329440]|0.1844,0.1844,[329440]|0.2558,0.2558,[329440]|0.1844,0.1844,[329440]|0.2483,0.2483,[329440]|0.2385,0.2385,[329440]|0.1266,0.1266,[329440]|0.1322,0.1322,[329440]|0.1205,0.1205,[329440]|0.0965,0.0965,[329440]|0.0832,0.0832,[329440]|0.0744,0.0744,[329440]|0.0813,0.0813,[329440]|0.0677,0.0677,[329440]|0.0832,0.0832,[329440]|0.0478,0.0478,[329440]|0.0813,0.0813,[329440]|0.0813,0.0813,[329440]|0.1766,0.1766,[329440]|0.1958,0.1958,[329440]|0.2209,0.2209,[329440]|0.2255,0.2255,[329440]|0.1566,0.1566,[329440]|0.208,0.208,[329440]|0.2209,0.2209,[329440]|0.2292,0.2292,[329440]|0.3668,0.3668,[329440]|0.3939,0.3939,[329440]|0.3263,0.3263,[329440]|0.3717,0.3717,[329440]|0.4513,0.4513,[329440]|0.4825,0.4825,[329440]|0.4245,0.4245,[329440]|0.3762,0.3762,[329440]|0.3399,0.3399,[329440]|0.3885,0.3885,[329440]|0.3053,0.3053,[329440]|0.2531,0.2531,[329440]|0.2385,0.2385,[329440]|0.1635,0.1635,[329440]|0.2041,0.2041,[329440]|0.208,0.208,[329440]|0.2865,0.2865,[329440]|0.3668,0.3668,[329440]|0.2865,0.2865,[329440]|0.27,0.27,[329440]|0.1805,0.1805,[329440]|0.1998,0.1998,[329440]|0.2602,0.2602,[329440]|0.2209,0.2209,[329440]|0.1766,0.1766,[329440]|0.1958,0.1958,[329440]|0.2209,0.2209,[329440]|0.2913,0.2913,[329440]|0.2913,0.2913,[329440]|0.2385,0.2385,[329440]|0.3096,0.3096,[329440]|0.4078,0.4078,[329440]|0.4749,0.4749,[329440]|0.5846,0.5846,[329440]|0.59,0.59,[329440]|0.6334,0.6334,[329440]|0.6681,0.6681,[329440]|0.6906,0.6906,[329440]|0.7869,0.7869,[329440]|0.835,0.835,[329440]|
+
+SEQUENCE_REF   FER_CAPAA
+LINE_GRAPH     IUPredWS (Long) <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.247,0.247,[72144e]|0.3392,0.3392,[72144e]|0.2609,0.2609,[72144e]|0.3249,0.3249,[72144e]|0.2258,0.2258,[72144e]|0.2817,0.2817,[72144e]|0.1759,0.1759,[72144e]|0.2364,0.2364,[72144e]|0.2817,0.2817,[72144e]|0.3215,0.3215,[72144e]|0.2918,0.2918,[72144e]|0.2436,0.2436,[72144e]|0.1852,0.1852,[72144e]|0.1942,0.1942,[72144e]|0.2258,0.2258,[72144e]|0.2884,0.2884,[72144e]|0.2783,0.2783,[72144e]|0.3667,0.3667,[72144e]|0.4541,0.4541,[72144e]|0.4292,0.4292,[72144e]|0.3948,0.3948,[72144e]|0.3704,0.3704,[72144e]|0.391,0.391,[72144e]|0.2918,0.2918,[72144e]|0.3948,0.3948,[72144e]|0.2951,0.2951,[72144e]|0.3872,0.3872,[72144e]|0.2575,0.2575,[72144e]|0.3599,0.3599,[72144e]|0.3019,0.3019,[72144e]|0.2849,0.2849,[72144e]|0.2645,0.2645,[72144e]|0.2034,0.2034,[72144e]|0.2752,0.2752,[72144e]|0.3356,0.3356,[72144e]|0.2918,0.2918,[72144e]|0.247,0.247,[72144e]|0.2364,0.2364,[72144e]|0.247,0.247,[72144e]|0.1643,0.1643,[72144e]|0.1275,0.1275,[72144e]|0.1449,0.1449,[72144e]|0.1449,0.1449,[72144e]|0.1323,0.1323,[72144e]|0.0888,0.0888,[72144e]|0.1449,0.1449,[72144e]|0.1275,0.1275,[72144e]|0.1881,0.1881,[72144e]|0.2064,0.2064,[72144e]|0.3149,0.3149,[72144e]|0.3286,0.3286,[72144e]|0.268,0.268,[72144e]|0.2034,0.2034,[72144e]|0.2224,0.2224,[72144e]|0.3494,0.3494,[72144e]|0.3704,0.3704,[72144e]|0.3807,0.3807,[72144e]|0.422,0.422,[72144e]|0.4725,0.4725,[72144e]|0.5017,0.5017,[72144e]|0.5176,0.5176,[72144e]|0.5176,0.5176,[72144e]|0.4901,0.4901,[72144e]|0.422,0.422,[72144e]|0.422,0.422,[72144e]|0.3356,0.3356,[72144e]|0.3356,0.3356,[72144e]|0.2951,0.2951,[72144e]|0.2129,0.2129,[72144e]|0.2436,0.2436,[72144e]|0.2328,0.2328,[72144e]|0.2328,0.2328,[72144e]|0.247,0.247,[72144e]|0.2849,0.2849,[72144e]|0.3494,0.3494,[72144e]|0.2609,0.2609,[72144e]|0.268,0.268,[72144e]|0.2541,0.2541,[72144e]|0.2328,0.2328,[72144e]|0.2849,0.2849,[72144e]|0.2884,0.2884,[72144e]|0.2364,0.2364,[72144e]|0.2609,0.2609,[72144e]|0.2645,0.2645,[72144e]|0.2645,0.2645,[72144e]|0.3286,0.3286,[72144e]|0.3215,0.3215,[72144e]|0.4186,0.4186,[72144e]|0.4582,0.4582,[72144e]|0.4725,0.4725,[72144e]|0.5533,0.5533,[72144e]|0.494,0.494,[72144e]|0.4652,0.4652,[72144e]|0.4476,0.4476,[72144e]|0.3983,0.3983,[72144e]|0.4619,0.4619,[72144e]|0.433,0.433,[72144e]|
+LINE_GRAPH     IUPredWS (Short)        <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.7724,0.7724,[329440]|0.7501,0.7501,[329440]|0.7111,0.7111,[329440]|0.6984,0.6984,[329440]|0.59,0.59,[329440]|0.5711,0.5711,[329440]|0.442,0.442,[329440]|0.4203,0.4203,[329440]|0.2786,0.2786,[329440]|0.27,0.27,[329440]|0.2385,0.2385,[329440]|0.3005,0.3005,[329440]|0.2385,0.2385,[329440]|0.2483,0.2483,[329440]|0.2167,0.2167,[329440]|0.2255,0.2255,[329440]|0.2657,0.2657,[329440]|0.3456,0.3456,[329440]|0.3717,0.3717,[329440]|0.3992,0.3992,[329440]|0.3847,0.3847,[329440]|0.3311,0.3311,[329440]|0.3225,0.3225,[329440]|0.27,0.27,[329440]|0.3668,0.3668,[329440]|0.2786,0.2786,[329440]|0.4037,0.4037,[329440]|0.3096,0.3096,[329440]|0.4116,0.4116,[329440]|0.2255,0.2255,[329440]|0.2041,0.2041,[329440]|0.1602,0.1602,[329440]|0.1998,0.1998,[329440]|0.2657,0.2657,[329440]|0.1921,0.1921,[329440]|0.2558,0.2558,[329440]|0.2483,0.2483,[329440]|0.1322,0.1322,[329440]|0.138,0.138,[329440]|0.124,0.124,[329440]|0.0991,0.0991,[329440]|0.0884,0.0884,[329440]|0.0771,0.0771,[329440]|0.0858,0.0858,[329440]|0.0701,0.0701,[329440]|0.0858,0.0858,[329440]|0.049,0.049,[329440]|0.0813,0.0813,[329440]|0.0813,0.0813,[329440]|0.1766,0.1766,[329440]|0.1998,0.1998,[329440]|0.2255,0.2255,[329440]|0.2255,0.2255,[329440]|0.1566,0.1566,[329440]|0.208,0.208,[329440]|0.2209,0.2209,[329440]|0.2292,0.2292,[329440]|0.3668,0.3668,[329440]|0.3939,0.3939,[329440]|0.3263,0.3263,[329440]|0.3717,0.3717,[329440]|0.4513,0.4513,[329440]|0.4825,0.4825,[329440]|0.4245,0.4245,[329440]|0.3762,0.3762,[329440]|0.3399,0.3399,[329440]|0.3885,0.3885,[329440]|0.3053,0.3053,[329440]|0.2531,0.2531,[329440]|0.2385,0.2385,[329440]|0.1635,0.1635,[329440]|0.2041,0.2041,[329440]|0.208,0.208,[329440]|0.2865,0.2865,[329440]|0.3668,0.3668,[329440]|0.2865,0.2865,[329440]|0.27,0.27,[329440]|0.1805,0.1805,[329440]|0.1998,0.1998,[329440]|0.2602,0.2602,[329440]|0.2209,0.2209,[329440]|0.1766,0.1766,[329440]|0.1958,0.1958,[329440]|0.2209,0.2209,[329440]|0.2913,0.2913,[329440]|0.2913,0.2913,[329440]|0.2385,0.2385,[329440]|0.3096,0.3096,[329440]|0.4078,0.4078,[329440]|0.4749,0.4749,[329440]|0.5846,0.5846,[329440]|0.59,0.59,[329440]|0.6334,0.6334,[329440]|0.6681,0.6681,[329440]|0.6906,0.6906,[329440]|0.7869,0.7869,[329440]|0.835,0.835,[329440]|
+
+SEQUENCE_REF   Q93XJ9_SOLTU
+LINE_GRAPH     IUPredWS (Long) <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.3182,0.3182,[72144e]|0.2002,0.2002,[72144e]|0.1449,0.1449,[72144e]|0.2164,0.2164,[72144e]|0.2503,0.2503,[72144e]|0.268,0.268,[72144e]|0.3286,0.3286,[72144e]|0.2951,0.2951,[72144e]|0.2609,0.2609,[72144e]|0.2849,0.2849,[72144e]|0.3053,0.3053,[72144e]|0.2609,0.2609,[72144e]|0.2817,0.2817,[72144e]|0.2541,0.2541,[72144e]|0.2575,0.2575,[72144e]|0.2575,0.2575,[72144e]|0.2645,0.2645,[72144e]|0.2064,0.2064,[72144e]|0.2292,0.2292,[72144e]|0.3149,0.3149,[72144e]|0.2884,0.2884,[72144e]|0.2164,0.2164,[72144e]|0.1399,0.1399,[72144e]|0.2129,0.2129,[72144e]|0.2094,0.2094,[72144e]|0.1731,0.1731,[72144e]|0.1702,0.1702,[72144e]|0.1759,0.1759,[72144e]|0.1501,0.1501,[72144e]|0.2002,0.2002,[72144e]|0.247,0.247,[72144e]|0.2436,0.2436,[72144e]|0.1823,0.1823,[72144e]|0.2503,0.2503,[72144e]|0.1583,0.1583,[72144e]|0.1611,0.1611,[72144e]|0.2002,0.2002,[72144e]|0.2002,0.2002,[72144e]|0.1298,0.1298,[72144e]|0.1643,0.1643,[72144e]|0.1275,0.1275,[72144e]|0.107,0.107,[72144e]|0.087,0.087,[72144e]|0.087,0.087,[72144e]|0.1501,0.1501,[72144e]|0.1759,0.1759,[72144e]|0.2503,0.2503,[72144e]|0.2609,0.2609,[72144e]|0.2918,0.2918,[72144e]|0.2258,0.2258,[72144e]|0.2436,0.2436,[72144e]|0.1554,0.1554,[72144e]|0.1731,0.1731,[72144e]|0.0948,0.0948,[72144e]|0.1611,0.1611,[72144e]|0.1702,0.1702,[72144e]|0.2849,0.2849,[72144e]|0.2609,0.2609,[72144e]|0.2094,0.2094,[72144e]|0.1554,0.1554,[72144e]|0.1671,0.1671,[72144e]|0.1852,0.1852,[72144e]|0.2436,0.2436,[72144e]|0.2258,0.2258,[72144e]|0.3117,0.3117,[72144e]|0.3983,0.3983,[72144e]|0.4186,0.4186,[72144e]|0.3872,0.3872,[72144e]|0.374,0.374,[72144e]|0.3872,0.3872,[72144e]|0.2918,0.2918,[72144e]|0.391,0.391,[72144e]|0.2918,0.2918,[72144e]|0.384,0.384,[72144e]|0.2541,0.2541,[72144e]|0.3631,0.3631,[72144e]|0.3053,0.3053,[72144e]|0.2918,0.2918,[72144e]|0.2783,0.2783,[72144e]|0.2193,0.2193,[72144e]|0.2951,0.2951,[72144e]|0.3599,0.3599,[72144e]|0.3149,0.3149,[72144e]|0.2752,0.2752,[72144e]|0.2645,0.2645,[72144e]|0.2817,0.2817,[72144e]|0.2094,0.2094,[72144e]|0.1942,0.1942,[72144e]|0.1528,0.1528,[72144e]|0.1528,0.1528,[72144e]|0.1554,0.1554,[72144e]|0.1092,0.1092,[72144e]|0.1671,0.1671,[72144e]|0.1501,0.1501,[72144e]|0.2164,0.2164,[72144e]|0.2292,0.2292,[72144e]|0.3392,0.3392,[72144e]|0.3249,0.3249,[72144e]|0.2645,0.2645,[72144e]|0.2034,0.2034,[72144e]|0.2164,0.2164,[72144e]|0.3356,0.3356,[72144e]|0.3494,0.3494,[72144e]|0.3599,0.3599,[72144e]|0.494,0.494,[72144e]|0.494,0.494,[72144e]|0.4652,0.4652,[72144e]|0.4766,0.4766,[72144e]|0.4369,0.4369,[72144e]|0.3872,0.3872,[72144e]|0.3494,0.3494,[72144e]|0.3529,0.3529,[72144e]|0.2292,0.2292,[72144e]|0.2328,0.2328,[72144e]|0.2002,0.2002,[72144e]|0.1349,0.1349,[72144e]|0.1611,0.1611,[72144e]|0.1399,0.1399,[72144e]|0.0676,0.0676,[72144e]|0.078,0.078,[72144e]|0.1007,0.1007,[72144e]|0.1424,0.1424,[72144e]|0.0948,0.0948,[72144e]|0.0985,0.0985,[72144e]|0.0929,0.0929,[72144e]|0.0851,0.0851,[72144e]|0.0676,0.0676,[72144e]|0.0909,0.0909,[72144e]|0.1229,0.1229,[72144e]|0.1399,0.1399,[72144e]|0.1583,0.1583,[72144e]|0.1969,0.1969,[72144e]|0.2364,0.2364,[72144e]|0.2292,0.2292,[72144e]|0.3321,0.3321,[72144e]|0.3667,0.3667,[72144e]|0.3774,0.3774,[72144e]|0.4441,0.4441,[72144e]|0.3872,0.3872,[72144e]|0.384,0.384,[72144e]|0.5577,0.5577,[72144e]|0.5176,0.5176,[72144e]|0.6043,0.6043,[72144e]|0.5854,0.5854,[72144e]|
+LINE_GRAPH     IUPredWS (Short)        <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.8311,0.8311,[329440]|0.7912,0.7912,[329440]|0.7501,0.7501,[329440]|0.6255,0.6255,[329440]|0.5008,0.5008,[329440]|0.4825,0.4825,[329440]|0.4513,0.4513,[329440]|0.4078,0.4078,[329440]|0.3885,0.3885,[329440]|0.2786,0.2786,[329440]|0.1732,0.1732,[329440]|0.1921,0.1921,[329440]|0.2292,0.2292,[329440]|0.1635,0.1635,[329440]|0.2385,0.2385,[329440]|0.2041,0.2041,[329440]|0.138,0.138,[329440]|0.138,0.138,[329440]|0.1566,0.1566,[329440]|0.1698,0.1698,[329440]|0.1698,0.1698,[329440]|0.1698,0.1698,[329440]|0.138,0.138,[329440]|0.1566,0.1566,[329440]|0.1456,0.1456,[329440]|0.1266,0.1266,[329440]|0.0744,0.0744,[329440]|0.0744,0.0744,[329440]|0.0621,0.0621,[329440]|0.0965,0.0965,[329440]|0.1416,0.1416,[329440]|0.138,0.138,[329440]|0.1349,0.1349,[329440]|0.2041,0.2041,[329440]|0.138,0.138,[329440]|0.1667,0.1667,[329440]|0.1635,0.1635,[329440]|0.138,0.138,[329440]|0.1117,0.1117,[329440]|0.1635,0.1635,[329440]|0.1088,0.1088,[329440]|0.1041,0.1041,[329440]|0.0884,0.0884,[329440]|0.1266,0.1266,[329440]|0.1416,0.1416,[329440]|0.1018,0.1018,[329440]|0.1495,0.1495,[329440]|0.1732,0.1732,[329440]|0.1805,0.1805,[329440]|0.1805,0.1805,[329440]|0.2041,0.2041,[329440]|0.1566,0.1566,[329440]|0.1732,0.1732,[329440]|0.1117,0.1117,[329440]|0.1766,0.1766,[329440]|0.0991,0.0991,[329440]|0.1805,0.1805,[329440]|0.2292,0.2292,[329440]|0.2865,0.2865,[329440]|0.2292,0.2292,[329440]|0.2432,0.2432,[329440]|0.2041,0.2041,[329440]|0.2122,0.2122,[329440]|0.2432,0.2432,[329440]|0.3184,0.3184,[329440]|0.3535,0.3535,[329440]|0.3762,0.3762,[329440]|0.363,0.363,[329440]|0.3762,0.3762,[329440]|0.3717,0.3717,[329440]|0.3225,0.3225,[329440]|0.4078,0.4078,[329440]|0.3359,0.3359,[329440]|0.4458,0.4458,[329440]|0.3668,0.3668,[329440]|0.4879,0.4879,[329440]|0.3096,0.3096,[329440]|0.2865,0.2865,[329440]|0.2385,0.2385,[329440]|0.2865,0.2865,[329440]|0.3578,0.3578,[329440]|0.2865,0.2865,[329440]|0.3491,0.3491,[329440]|0.3359,0.3359,[329440]|0.208,0.208,[329440]|0.2167,0.2167,[329440]|0.1958,0.1958,[329440]|0.1635,0.1635,[329440]|0.1117,0.1117,[329440]|0.1088,0.1088,[329440]|0.1041,0.1041,[329440]|0.0858,0.0858,[329440]|0.1117,0.1117,[329440]|0.0643,0.0643,[329440]|0.1041,0.1041,[329440]|0.1041,0.1041,[329440]|0.2122,0.2122,[329440]|0.2292,0.2292,[329440]|0.2483,0.2483,[329440]|0.2333,0.2333,[329440]|0.1602,0.1602,[329440]|0.208,0.208,[329440]|0.2167,0.2167,[329440]|0.2209,0.2209,[329440]|0.3491,0.3491,[329440]|0.3717,0.3717,[329440]|0.3885,0.3885,[329440]|0.3806,0.3806,[329440]|0.3992,0.3992,[329440]|0.4116,0.4116,[329440]|0.3668,0.3668,[329440]|0.3263,0.3263,[329440]|0.2748,0.2748,[329440]|0.3225,0.3225,[329440]|0.2122,0.2122,[329440]|0.1635,0.1635,[329440]|0.1495,0.1495,[329440]|0.0991,0.0991,[329440]|0.1322,0.1322,[329440]|0.1292,0.1292,[329440]|0.1117,0.1117,[329440]|0.1667,0.1667,[329440]|0.1117,0.1117,[329440]|0.1018,0.1018,[329440]|0.0607,0.0607,[329440]|0.0723,0.0723,[329440]|0.0587,0.0587,[329440]|0.0643,0.0643,[329440]|0.0643,0.0643,[329440]|0.0771,0.0771,[329440]|0.1292,0.1292,[329440]|0.1766,0.1766,[329440]|0.1667,0.1667,[329440]|0.1667,0.1667,[329440]|0.2255,0.2255,[329440]|0.3225,0.3225,[329440]|0.3885,0.3885,[329440]|0.5008,0.5008,[329440]|0.5008,0.5008,[329440]|0.5667,0.5667,[329440]|0.7079,0.7079,[329440]|0.7342,0.7342,[329440]|0.835,0.835,[329440]|0.8746,0.8746,[329440]|
+
+SEQUENCE_REF   FER1_SOLLC
+LINE_GRAPH     IUPredWS (Long) <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.3286,0.3286,[72144e]|0.2094,0.2094,[72144e]|0.1528,0.1528,[72144e]|0.2258,0.2258,[72144e]|0.2609,0.2609,[72144e]|0.2752,0.2752,[72144e]|0.3356,0.3356,[72144e]|0.3249,0.3249,[72144e]|0.2918,0.2918,[72144e]|0.3149,0.3149,[72144e]|0.3321,0.3321,[72144e]|0.2884,0.2884,[72144e]|0.3087,0.3087,[72144e]|0.2849,0.2849,[72144e]|0.2849,0.2849,[72144e]|0.2849,0.2849,[72144e]|0.2951,0.2951,[72144e]|0.2364,0.2364,[72144e]|0.2575,0.2575,[72144e]|0.3426,0.3426,[72144e]|0.3149,0.3149,[72144e]|0.247,0.247,[72144e]|0.1643,0.1643,[72144e]|0.2436,0.2436,[72144e]|0.2399,0.2399,[72144e]|0.2034,0.2034,[72144e]|0.2002,0.2002,[72144e]|0.2064,0.2064,[72144e]|0.1823,0.1823,[72144e]|0.2094,0.2094,[72144e]|0.2609,0.2609,[72144e]|0.2575,0.2575,[72144e]|0.1942,0.1942,[72144e]|0.2645,0.2645,[72144e]|0.1759,0.1759,[72144e]|0.1791,0.1791,[72144e]|0.2193,0.2193,[72144e]|0.2193,0.2193,[72144e]|0.1476,0.1476,[72144e]|0.1852,0.1852,[72144e]|0.1424,0.1424,[72144e]|0.1206,0.1206,[72144e]|0.0985,0.0985,[72144e]|0.0985,0.0985,[72144e]|0.1671,0.1671,[72144e]|0.1942,0.1942,[72144e]|0.2817,0.2817,[72144e]|0.2918,0.2918,[72144e]|0.3215,0.3215,[72144e]|0.2575,0.2575,[72144e]|0.2752,0.2752,[72144e]|0.1823,0.1823,[72144e]|0.2034,0.2034,[72144e]|0.1206,0.1206,[72144e]|0.1969,0.1969,[72144e]|0.2034,0.2034,[72144e]|0.3182,0.3182,[72144e]|0.2951,0.2951,[72144e]|0.2436,0.2436,[72144e]|0.1852,0.1852,[72144e]|0.1969,0.1969,[72144e]|0.2193,0.2193,[72144e]|0.2817,0.2817,[72144e]|0.2645,0.2645,[72144e]|0.3494,0.3494,[72144e]|0.4369,0.4369,[72144e]|0.4541,0.4541,[72144e]|0.422,0.422,[72144e]|0.4017,0.4017,[72144e]|0.4186,0.4186,[72144e]|0.3215,0.3215,[72144e]|0.422,0.422,[72144e]|0.3215,0.3215,[72144e]|0.4119,0.4119,[72144e]|0.2884,0.2884,[72144e]|0.391,0.391,[72144e]|0.3321,0.3321,[72144e]|0.3182,0.3182,[72144e]|0.3053,0.3053,[72144e]|0.2541,0.2541,[72144e]|0.3286,0.3286,[72144e]|0.391,0.391,[72144e]|0.3529,0.3529,[72144e]|0.3117,0.3117,[72144e]|0.3019,0.3019,[72144e]|0.3182,0.3182,[72144e]|0.247,0.247,[72144e]|0.2292,0.2292,[72144e]|0.1852,0.1852,[72144e]|0.1852,0.1852,[72144e]|0.1823,0.1823,[72144e]|0.1298,0.1298,[72144e]|0.1942,0.1942,[72144e]|0.1759,0.1759,[72144e]|0.2436,0.2436,[72144e]|0.2609,0.2609,[72144e]|0.3631,0.3631,[72144e]|0.3667,0.3667,[72144e]|0.3087,0.3087,[72144e]|0.247,0.247,[72144e]|0.2609,0.2609,[72144e]|0.384,0.384,[72144e]|0.3983,0.3983,[72144e]|0.4087,0.4087,[72144e]|0.5419,0.5419,[72144e]|0.5419,0.5419,[72144e]|0.5139,0.5139,[72144e]|0.5211,0.5211,[72144e]|0.4831,0.4831,[72144e]|0.4292,0.4292,[72144e]|0.3948,0.3948,[72144e]|0.3983,0.3983,[72144e]|0.2884,0.2884,[72144e]|0.2884,0.2884,[72144e]|0.2541,0.2541,[72144e]|0.1791,0.1791,[72144e]|0.2094,0.2094,[72144e]|0.1823,0.1823,[72144e]|0.1823,0.1823,[72144e]|0.1881,0.1881,[72144e]|0.2224,0.2224,[72144e]|0.2884,0.2884,[72144e]|0.2164,0.2164,[72144e]|0.2164,0.2164,[72144e]|0.2064,0.2064,[72144e]|0.1942,0.1942,[72144e]|0.1643,0.1643,[72144e]|0.2064,0.2064,[72144e]|0.2541,0.2541,[72144e]|0.2783,0.2783,[72144e]|0.3019,0.3019,[72144e]|0.3494,0.3494,[72144e]|0.391,0.391,[72144e]|0.3807,0.3807,[72144e]|0.4864,0.4864,[72144e]|0.5342,0.5342,[72144e]|0.5533,0.5533,[72144e]|0.6576,0.6576,[72144e]|0.5901,0.5901,[72144e]|0.6043,0.6043,[72144e]|0.5951,0.5951,[72144e]|0.5493,0.5493,[72144e]|0.6427,0.6427,[72144e]|0.6227,0.6227,[72144e]|
+LINE_GRAPH     IUPredWS (Short)        <html>Protein Disorder with IUPredWS - raw scores<br/>Above 0.5 indicates disorder</html>       0.8391,0.8391,[329440]|0.8001,0.8001,[329440]|0.7573,0.7573,[329440]|0.6334,0.6334,[329440]|0.5173,0.5173,[329440]|0.5008,0.5008,[329440]|0.4703,0.4703,[329440]|0.4245,0.4245,[329440]|0.4116,0.4116,[329440]|0.3263,0.3263,[329440]|0.2167,0.2167,[329440]|0.2385,0.2385,[329440]|0.2786,0.2786,[329440]|0.2041,0.2041,[329440]|0.2865,0.2865,[329440]|0.2531,0.2531,[329440]|0.1805,0.1805,[329440]|0.1766,0.1766,[329440]|0.1958,0.1958,[329440]|0.2122,0.2122,[329440]|0.208,0.208,[329440]|0.2122,0.2122,[329440]|0.1766,0.1766,[329440]|0.1921,0.1921,[329440]|0.1844,0.1844,[329440]|0.1602,0.1602,[329440]|0.0991,0.0991,[329440]|0.1018,0.1018,[329440]|0.0858,0.0858,[329440]|0.1041,0.1041,[329440]|0.1566,0.1566,[329440]|0.1495,0.1495,[329440]|0.1495,0.1495,[329440]|0.2167,0.2167,[329440]|0.1495,0.1495,[329440]|0.1766,0.1766,[329440]|0.1732,0.1732,[329440]|0.1456,0.1456,[329440]|0.1205,0.1205,[329440]|0.1732,0.1732,[329440]|0.115,0.115,[329440]|0.1088,0.1088,[329440]|0.0935,0.0935,[329440]|0.1292,0.1292,[329440]|0.1456,0.1456,[329440]|0.1018,0.1018,[329440]|0.1532,0.1532,[329440]|0.1732,0.1732,[329440]|0.1878,0.1878,[329440]|0.1878,0.1878,[329440]|0.2122,0.2122,[329440]|0.1602,0.1602,[329440]|0.1766,0.1766,[329440]|0.1178,0.1178,[329440]|0.1844,0.1844,[329440]|0.1018,0.1018,[329440]|0.1844,0.1844,[329440]|0.2333,0.2333,[329440]|0.2913,0.2913,[329440]|0.2333,0.2333,[329440]|0.2483,0.2483,[329440]|0.208,0.208,[329440]|0.2167,0.2167,[329440]|0.2531,0.2531,[329440]|0.3263,0.3263,[329440]|0.3578,0.3578,[329440]|0.3806,0.3806,[329440]|0.3668,0.3668,[329440]|0.3762,0.3762,[329440]|0.3717,0.3717,[329440]|0.3225,0.3225,[329440]|0.4116,0.4116,[329440]|0.3399,0.3399,[329440]|0.4513,0.4513,[329440]|0.3717,0.3717,[329440]|0.4879,0.4879,[329440]|0.3146,0.3146,[329440]|0.2865,0.2865,[329440]|0.2385,0.2385,[329440]|0.2865,0.2865,[329440]|0.363,0.363,[329440]|0.2913,0.2913,[329440]|0.3535,0.3535,[329440]|0.3359,0.3359,[329440]|0.2122,0.2122,[329440]|0.2209,0.2209,[329440]|0.1998,0.1998,[329440]|0.1667,0.1667,[329440]|0.115,0.115,[329440]|0.115,0.115,[329440]|0.106,0.106,[329440]|0.0884,0.0884,[329440]|0.1205,0.1205,[329440]|0.0723,0.0723,[329440]|0.115,0.115,[329440]|0.115,0.115,[329440]|0.2292,0.2292,[329440]|0.2558,0.2558,[329440]|0.2786,0.2786,[329440]|0.2786,0.2786,[329440]|0.1958,0.1958,[329440]|0.2558,0.2558,[329440]|0.27,0.27,[329440]|0.2865,0.2865,[329440]|0.4149,0.4149,[329440]|0.442,0.442,[329440]|0.4651,0.4651,[329440]|0.46,0.46,[329440]|0.4781,0.4781,[329440]|0.4879,0.4879,[329440]|0.4513,0.4513,[329440]|0.4078,0.4078,[329440]|0.3491,0.3491,[329440]|0.3992,0.3992,[329440]|0.3146,0.3146,[329440]|0.2602,0.2602,[329440]|0.2385,0.2385,[329440]|0.1698,0.1698,[329440]|0.2167,0.2167,[329440]|0.1921,0.1921,[329440]|0.2748,0.2748,[329440]|0.3456,0.3456,[329440]|0.27,0.27,[329440]|0.2432,0.2432,[329440]|0.1667,0.1667,[329440]|0.1844,0.1844,[329440]|0.1635,0.1635,[329440]|0.1805,0.1805,[329440]|0.1844,0.1844,[329440]|0.2041,0.2041,[329440]|0.2913,0.2913,[329440]|0.3535,0.3535,[329440]|0.3399,0.3399,[329440]|0.3399,0.3399,[329440]|0.3806,0.3806,[329440]|0.4781,0.4781,[329440]|0.5374,0.5374,[329440]|0.6442,0.6442,[329440]|0.6442,0.6442,[329440]|0.7111,0.7111,[329440]|0.7458,0.7458,[329440]|0.7724,0.7724,[329440]|0.865,0.865,[329440]|0.9009,0.9009,[329440]|
+
+COLOUR IUPredWS (Long) 72144e
+COLOUR IUPredWS (Short)        329440
+COLOUR IUPredWS (Long) 72144e
+COLOUR IUPredWS (Short)        329440
+COLOUR IUPredWS (Long) 72144e
+COLOUR IUPredWS (Short)        329440
+COLOUR IUPredWS (Long) 72144e
+COLOUR IUPredWS (Short)        329440
+COLOUR IUPredWS (Long) 72144e
+COLOUR IUPredWS (Short)        329440
+COLOUR IUPredWS (Long) 72144e
+COLOUR IUPredWS (Short)        329440
+COLOUR IUPredWS (Long) 72144e
+COLOUR IUPredWS (Short)        329440
+COLOUR IUPredWS (Long) 72144e
+COLOUR IUPredWS (Short)        329440
+COLOUR IUPredWS (Long) 72144e
+COLOUR IUPredWS (Short)        329440
+COLOUR IUPredWS (Long) 72144e
+COLOUR IUPredWS (Short)        329440
+COLOUR IUPredWS (Long) 72144e
+COLOUR IUPredWS (Short)        329440
+COLOUR IUPredWS (Long) 72144e
+COLOUR IUPredWS (Short)        329440
+COLOUR IUPredWS (Long) 72144e
+COLOUR IUPredWS (Short)        329440
+COLOUR IUPredWS (Long) 72144e
+COLOUR IUPredWS (Short)        329440
+COLOUR IUPredWS (Long) 72144e
+COLOUR IUPredWS (Short)        329440
+GRAPHLINE      IUPredWS (Long) 0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Short)        0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Long) 0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Short)        0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Long) 0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Short)        0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Long) 0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Short)        0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Long) 0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Short)        0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Long) 0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Short)        0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Long) 0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Short)        0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Long) 0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Short)        0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Long) 0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Short)        0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Long) 0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Short)        0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Long) 0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Short)        0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Long) 0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Short)        0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Long) 0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Short)        0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Long) 0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Short)        0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Long) 0.5     Above 0.5 indicates disorder    ff0000
+GRAPHLINE      IUPredWS (Short)        0.5     Above 0.5 indicates disorder    ff0000
+COMBINE        IUPredWS (Long) IUPredWS (Short)
+
+SEQUENCE_REF   Q93XJ9_SOLTU
+COMBINE        IUPredWS (Long) IUPredWS (Short)
+
+SEQUENCE_REF   FER_CAPAA
+COMBINE        IUPredWS (Long) IUPredWS (Short)
+
+SEQUENCE_REF   FER_CAPAN
+COMBINE        IUPredWS (Long) IUPredWS (Short)
+
+SEQUENCE_REF   FER1_MESCR
+COMBINE        IUPredWS (Long) IUPredWS (Short)
+
+SEQUENCE_REF   FER1_SPIOL
+COMBINE        IUPredWS (Long) IUPredWS (Short)
+
+SEQUENCE_REF   FER1_PEA
+COMBINE        IUPredWS (Long) IUPredWS (Short)
+
+SEQUENCE_REF   Q7XA98_TRIPR
+COMBINE        IUPredWS (Long) IUPredWS (Short)
+
+SEQUENCE_REF   O80429_MAIZE
+COMBINE        IUPredWS (Long) IUPredWS (Short)
+
+SEQUENCE_REF   FER1_MAIZE
+COMBINE        IUPredWS (Long) IUPredWS (Short)
+
+SEQUENCE_REF   FER3_RAPSA
+COMBINE        IUPredWS (Long) IUPredWS (Short)
+
+SEQUENCE_REF   FER_BRANA
+COMBINE        IUPredWS (Long) IUPredWS (Short)
+
+SEQUENCE_REF   FER1_ARATH
+COMBINE        IUPredWS (Long) IUPredWS (Short)
+
+SEQUENCE_REF   Q93Z60_ARATH
+COMBINE        IUPredWS (Long) IUPredWS (Short)
+
+SEQUENCE_REF   FER2_ARATH
+COMBINE        IUPredWS (Long) IUPredWS (Short)
+
+SEQUENCE_REF   FER1_SOLLC

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index fa6d3dd..17c2c8b 100755 (executable)
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -132,13 +132,13 @@ GRAPHLINE&#9;<em>graph_name</em>&#9;<em>value</em>&#9;<em>label</em>&#9;<em>colo
 </ul></p>
 <h3><font face="Arial, Helvetica, sans-serif">(Since Jalview 2.2.1) SEQUENCE_GROUP</font></h3>
 <p>Groups of sequences can be defined using the tab delimited line</p>
-<pre>SEQUENCE_GROUP    Group_Name      Group_Start     Group_End       Sequences</pre>
+<pre>SEQUENCE_GROUP    Group_Name      Group_Start     Group_End       <em>Sequences</em></pre>
 <p>The sequences can be defined by alignment index and a range of sequences can 
   be defined in a comma delimited field such as</p>
 <p>2-5,8-15,20,22</p>
 <p>Enter * to select all groups. </p>
-<p>If the alignment indices are not known, enter -1 then a tab delimited list 
-  of sequence ids. </p>
+<p><strong>Note:</strong> If the alignment indices are not known, enter -1, followed by a tab and then a tab delimited list 
+specifying the sequence ids. </p>
 <p>If the SEQUENCE_REF has been defined, the group_start and group_end will be 
   relative to the sequence residue numbering, otherwise the group_start and group_end 
   will be the alignment column indices. </p>
@@ -197,13 +197,14 @@ COLOUR&#9;Purple Letters&#9;151,52,228
 COMBINE&#9;Green Values&#9;Red Values
 GRAPHLINE&#9;Red Values&#9;2.6&#9;threshold&#9;black
 
-SEQUENCE_GROUP Group_A 30 50 *
-SEQUENCE_GROUP Group_B 1 351 2-5
-SEQUENCE_GROUP Group_C 12 14 -1 seq1   seq2    seq3
-PROPERTIES Group_A description=This is the description colour=Helix Propensity pidThreshold=0 outlineColour=red displayBoxes=true displayText=false    colourText=false textCol1=black textCol2=black textColThreshold=0
-PROPERTIES Group_B outlineColour=red
-PROPERTIES Group_C colour=Clustal
+SEQUENCE_GROUP&#9;Group_A&#9;30&#9;50&#9;*
+SEQUENCE_GROUP&#9;Group_B&#9;1&#9;351&#9;2-5
+SEQUENCE_GROUP&#9;Group_C&#9;12&#9;14&#9;-1&#9;seq1&#9;seq2&#9;seq3
+PROPERTIES&#9;Group_A&#9;description=This is the description&#9;colour=Helix Propensity&#9;pidThreshold=0&#9;outlineColour=red&#9;displayBoxes=true&#9;displayText=false&#9;colourText=false&#9;textCol1=black&#9;textCol2=black&#9;textColThreshold=0
+PROPERTIES&#9;Group_B&#9;outlineColour=red
+PROPERTIES&#9;Group_C&#9;colour=Clustal
 </pre>
 </p>
+<p><em>Last updated for version 2.8.1</em></p>
 </body>
 </html>

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 540a0e0..f63cb76 100755 (executable)
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -653,4 +653,16 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
   {
     return imgWidth;
   }
+  private int[] bounds = new int[2];
+  @Override
+  public int[] getVisibleVRange()
+  {
+    if (ap!=null && ap.alabels!=null)
+    {
+    int sOffset=-ap.alabels.scrollOffset;
+    int visHeight = sOffset+ap.annotationPanelHolder.getHeight();
+    bounds[0] = sOffset; bounds[1]=visHeight;
+    return bounds;
+    } else return null;
+  }
 }

diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index 042e0f7..e99c321 100755 (executable)
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -17,33 +17,35 @@
  */
 package jalview.datamodel;
 
-import java.awt.*;
+import java.awt.Color;
 
 /**
- * DOCUMENT ME!
+ * Holds all annotation values for a position in an AlignmentAnnotation row
  * 
  * @author $author$
  * @version $Revision$
  */
 public class Annotation
 {
-  /** DOCUMENT ME!! */
+  /** Character label - also shown below histogram */
   public String displayCharacter = "";
 
-  /** DOCUMENT ME!! */
-  public String description = ""; // currently used as mouse over
+  /**
+   * Text label for position: shown in mouse over and displayed on secondary
+   * structure glyphs
+   */
+  public String description = "";
 
-  /** DOCUMENT ME!! */
-  public char secondaryStructure = ' '; // recognises H, E and S(?)
+  /**
+   * Secondary structure symbol: Protein symbols are H, E and S(?), RNA are
+   * WUSS/Vienna plus extended pseudoknot symbols
+   */
+  public char secondaryStructure = ' ';
 
-  /** DOCUMENT ME!! */
+  /** Score for the position - used in histograms, line graphs and for shading */
   public float value;
   
-
-
-  // add visual cues here
-
-  /** DOCUMENT ME!! */
+  /** Colour for position */
   public Color colour;
 
   /**
@@ -121,8 +123,66 @@ public class Annotation
   {
     this(null, null, ' ', val,null);
   }
-  
-  
-  
-  
+
+  /**
+   * human readable representation of an annotation row element.
+   *
+   * Format is 'display Char','secondary Structure
+   * Char',"description",score,[colourstring]
+   *
+   * fields may be missing if they are null, whitespace, or equivalent to
+   * Float.NaN
+   */
+  @Override
+  public String toString()
+  {
+    StringBuffer sb = new StringBuffer();
+    if (displayCharacter != null)
+    {
+      sb.append("\'");
+      sb.append(displayCharacter);
+      sb.append("\'");
+    }
+    {
+      sb.append(",");
+    }
+    if (secondaryStructure != 0
+            && !("" + displayCharacter).equals("" + secondaryStructure))
+    {
+      sb.append("\'");
+      sb.append(secondaryStructure);
+      sb.append("\'");
+    }
+    {
+      sb.append(",");
+    }
+    if (description != null && description.length() > 0)
+    {
+      sb.append("\"");
+      sb.append(description);
+      sb.append("\"");
+    }
+    {
+      sb.append(",");
+    }
+    if (value != Float.NaN)
+    {
+      sb.append(value);
+    }
+    if (colour != null)
+    {
+      if (sb.length() > 0)
+      {
+        sb.append(",");
+      }
+      sb.append("[");
+      sb.append(colour.getRed());
+      sb.append(",");
+      sb.append(colour.getGreen());
+      sb.append(",");
+      sb.append(colour.getBlue());
+      sb.append("]");
+    }
+    return sb.toString();
+  }
 }

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index f8a2543..5f20808 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -688,7 +688,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
         seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
         scalePanel.repaint();
 
-        if (av.getShowAnnotation())
+        if (av.getShowAnnotation() && scrollX!=0)
         {
           annotationPanel.fastPaint(scrollX);
         }

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index dd6f190..8566e57 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -816,18 +816,32 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               RenderingHints.VALUE_ANTIALIAS_ON);
     }
 
-    drawComponent(g2, width);
+    drawComponent(g2, true, width);
 
   }
 
   /**
-   * DOCUMENT ME!
+   * Draw the full set of annotation Labels for the alignment at the given cursor
    * 
-   * @param g
-   *          DOCUMENT ME!
+   * @param g Graphics2D instance (needed for font scaling)
+   * @param width Width for scaling labels
+   *          
    */
   public void drawComponent(Graphics g, int width)
   {
+    drawComponent(g, false, width);
+  }
+
+  private final boolean debugRedraw = false;
+  /**
+   * Draw the full set of annotation Labels for the alignment at the given cursor
+   * 
+   * @param g Graphics2D instance (needed for font scaling)
+   * @param clip - true indicates that only current visible area needs to be rendered
+   * @param width Width for scaling labels         
+   */
+  public void drawComponent(Graphics g, boolean clip, int width)
+  {
     if (av.getFont().getSize() < 10)
     {
       g.setFont(font);
@@ -843,7 +857,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
     g.translate(0, scrollOffset);
     g.setColor(Color.black);
-
+    
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
     int fontHeight = g.getFont().getSize();
     int y = 0;
@@ -853,22 +867,54 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     Font baseFont = g.getFont();
     FontMetrics baseMetrics = fm;
     int ofontH = fontHeight;
-    boolean visible = true;
+    int sOffset=0;
+    int visHeight = 0;
+    int[] visr = (ap!=null && ap.annotationPanel!=null) ? ap.annotationPanel.getVisibleVRange() : null;
+    if (clip && visr!=null){ 
+      sOffset = visr[0]; 
+      visHeight = visr[1];
+    }
+    boolean visible = true,before=false,after=false;
     if (aa != null)
     {
       hasHiddenRows = false;
+      int olY=0;
       for (int i = 0; i < aa.length; i++)
       {
         visible = true;
-        g.setColor(Color.black);
-
         if (!aa[i].visible)
         {
           hasHiddenRows = true;
           continue;
         }
-
+        olY=y;
         y += aa[i].height;
+        if (clip) {if (y<sOffset)
+        {
+          if (!before)
+          {
+            if (debugRedraw) {
+              System.out.println("before vis: "+i);
+            }
+          before=true;
+          }
+          // don't draw what isn't visible
+          continue;
+        }
+        if (olY>visHeight)
+        {
+
+          if (!after)
+          {
+            if (debugRedraw) {
+              System.out.println("Scroll offset: "+sOffset+" after vis: "+i);
+            }
+          after=true;
+          }
+          // don't draw what isn't visible
+          continue;
+        }}
+        g.setColor(Color.black);
 
         offset = -aa[i].height / 2;
 
@@ -885,6 +931,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         if (aa[i].graphGroup > -1)
         {
           int groupSize = 0;
+          // TODO: JAL-1291 revise rendering model so the graphGroup map is computed efficiently for all visible labels
           for (int gg = 0; gg < aa.length; gg++)
           {
             if (aa[gg].graphGroup == aa[i].graphGroup)

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index d0af0a5..eb21dbc 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -760,7 +760,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
     if (imgWidth < 1)
       return;
-    if (image == null || imgWidth != image.getWidth()
+    if (image == null || imgWidth != image.getWidth(this)
             || image.getHeight(this) != getHeight())
     {
       try
@@ -800,7 +800,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     imageFresh = false;
     g.drawImage(image, 0, 0, this);
   }
-
+  /**
+   * set true to enable redraw timing debug output on stderr
+   */
+  private final boolean debugRedraw = false;
   /**
    * non-Thread safe repaint
    * 
@@ -809,7 +812,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
    */
   public void fastPaint(int horizontal)
   {
-
     if ((horizontal == 0) || gg == null
             || av.getAlignment().getAlignmentAnnotation() == null
             || av.getAlignment().getAlignmentAnnotation().length < 1
@@ -818,8 +820,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       repaint();
       return;
     }
+    long stime=System.currentTimeMillis();
     gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
-
+    long mtime=System.currentTimeMillis();
     int sr = av.startRes;
     int er = av.endRes + 1;
     int transX = 0;
@@ -839,9 +842,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     drawComponent(gg, sr, er);
 
     gg.translate(-transX, 0);
-
+    long dtime=System.currentTimeMillis();
     fastPaint = true;
     repaint();
+    long rtime=System.currentTimeMillis();
+    if (debugRedraw) {
+      System.err.println("Scroll:\t"+horizontal+"\tCopyArea:\t"+(mtime-stime)+"\tDraw component:\t"+(dtime-mtime)+"\tRepaint call:\t"+(rtime-dtime));
+    }
 
   }
 
@@ -902,7 +909,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       }
       fadedImage = null;
     }
-
+    
     g.setColor(Color.white);
     g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
 
@@ -950,4 +957,16 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   {
     return imgWidth;
   }
+  private int[] bounds = new int[2];
+  @Override
+  public int[] getVisibleVRange()
+  {
+    if (ap!=null && ap.alabels!=null)
+    {
+    int sOffset=-ap.alabels.scrollOffset;
+    int visHeight = sOffset+ap.annotationSpaceFillerHolder.getHeight();
+    bounds[0] = sOffset; bounds[1]=visHeight;
+    return bounds;
+    } else return null;
+  }
 }

diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index 014f076..21a2224 100755 (executable)
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -25,7 +25,8 @@ import java.awt.*;
 import jalview.datamodel.*;
 
 /**
- * DOCUMENT ME!
+ * Route datamodel/view update events for a sequence set to any display components involved
+ * TODO: JV3 refactor to abstract gui/view package
  * 
  * @author $author$
  * @version $Revision$

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 45e6c47..b3a22df 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -131,7 +131,9 @@ public class AnnotationFile
       StringBuffer colours = new StringBuffer();
       StringBuffer graphLine = new StringBuffer();
       StringBuffer rowprops = new StringBuffer();
-      Hashtable graphGroup = new Hashtable();
+      Hashtable<Integer,String> graphGroup = new Hashtable<Integer,String>();
+      Hashtable<Integer, Object[]> graphGroup_refs = new Hashtable<Integer,Object[]>();
+      BitSet graphGroupSeen = new BitSet();
 
       java.awt.Color color;
 
@@ -139,61 +141,20 @@ public class AnnotationFile
       {
         row = annotations[i];
 
-        if (!row.visible && !row.hasScore())
+        if (!row.visible && !row.hasScore() && !(row.graphGroup>-1 && graphGroupSeen.get(row.graphGroup)))
         {
           continue;
         }
 
         color = null;
         oneColour = true;
-
-        if (row.sequenceRef == null)
-        {
-          if (refSeq != null)
-          {
-            text.append(newline);
-            text.append("SEQUENCE_REF\tALIGNMENT");
-            text.append(newline);
-          }
-
-          refSeq = null;
-        }
-
-        else
-        {
-          if (refSeq == null || refSeq != row.sequenceRef)
-          {
-            refSeq = row.sequenceRef;
-            text.append(newline);
-            text.append("SEQUENCE_REF\t");
-            text.append(refSeq.getName());
-            text.append(newline);
-          }
-        }
+        
+        // mark any sequence references for the row
+        writeSequence_Ref(refSeq ,row.sequenceRef);
+        refSeq = row.sequenceRef;
         // mark any group references for the row
-        if (row.groupRef == null)
-        {
-
-          if (refGroup != null)
-          {
-            text.append(newline);
-            text.append("GROUP_REF\tALIGNMENT");
-            text.append(newline);
-          }
-
-          refGroup = null;
-        }
-        else
-        {
-          if (refGroup == null || refGroup != row.groupRef)
-          {
-            refGroup = row.groupRef;
-            text.append(newline);
-            text.append("GROUP_REF\t");
-            text.append(refGroup.getName());
-            text.append(newline);
-          }
-        }
+        writeGroup_Ref(refGroup, row.groupRef);
+        refGroup = row.groupRef;
 
         boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, hasValues = row.hasScore, hasText = false;
         // lookahead to check what the annotation row object actually contains.
@@ -251,13 +212,16 @@ public class AnnotationFile
 
           if (row.graphGroup > -1)
           {
-            String key = String.valueOf(row.graphGroup);
+            graphGroupSeen.set(row.graphGroup);
+            Integer key = new Integer(row.graphGroup);
             if (graphGroup.containsKey(key))
             {
               graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
+              
             }
             else
             {
+              graphGroup_refs.put(key, new Object[] { refSeq, refGroup});
               graphGroup.put(key, row.label);
             }
           }
@@ -382,13 +346,26 @@ public class AnnotationFile
       text.append(graphLine.toString());
       if (graphGroup.size() > 0)
       {
-        text.append("COMBINE\t");
-        Enumeration en = graphGroup.elements();
-        while (en.hasMoreElements())
-        {
-          text.append(en.nextElement());
+        SequenceI oldRefSeq = refSeq;
+        SequenceGroup oldRefGroup = refGroup;
+        for (Map.Entry<Integer, String> combine_statement:graphGroup.entrySet())
+        {
+          Object[] seqRefAndGroup=graphGroup_refs.get(combine_statement.getKey());
+          
+          writeSequence_Ref(refSeq, (SequenceI)seqRefAndGroup[0]);
+          refSeq = (SequenceI)seqRefAndGroup[0];
+          
+          writeGroup_Ref(refGroup, (SequenceGroup)seqRefAndGroup[1]);
+          refGroup = (SequenceGroup)seqRefAndGroup[1];
+          text.append("COMBINE\t");
+          text.append(combine_statement.getValue());
           text.append(newline);
         }
+        writeSequence_Ref(refSeq, oldRefSeq);
+        refSeq = oldRefSeq;
+        
+        writeGroup_Ref(refGroup, oldRefGroup);
+        refGroup = oldRefGroup;
       }
       text.append(rowprops.toString());
     }
@@ -419,6 +396,62 @@ public class AnnotationFile
     return text.toString();
   }
 
+  private Object writeGroup_Ref(SequenceGroup refGroup, SequenceGroup next_refGroup)
+  {
+    if (next_refGroup == null)
+    {
+
+      if (refGroup != null)
+      {
+        text.append(newline);
+        text.append("GROUP_REF\t");
+        text.append("ALIGNMENT");
+        text.append(newline);
+      }
+      return true;
+    }
+    else
+    {
+      if (refGroup == null || refGroup != next_refGroup)
+      {
+        text.append(newline);
+        text.append("GROUP_REF\t");
+        text.append(next_refGroup.getName());
+        text.append(newline);
+        return true;
+      }
+    }
+    return false;  
+  }
+  
+  private boolean writeSequence_Ref(SequenceI refSeq, SequenceI next_refSeq)
+  {
+
+    if (next_refSeq==null)
+    {
+      if (refSeq != null)
+      {
+        text.append(newline);
+        text.append("SEQUENCE_REF\t");
+        text.append("ALIGNMENT");
+        text.append(newline);
+        return true;
+      }
+    }
+    else
+    {
+      if (refSeq == null || refSeq != next_refSeq)
+      {
+        text.append(newline);
+        text.append("SEQUENCE_REF\t");
+        text.append(next_refSeq.getName());
+        text.append(newline);
+        return true;
+      }
+    }
+    return false;
+  }
+
   public void printGroups(List<SequenceGroup> list)
   {
     SequenceI seqrep = null;
@@ -579,14 +612,20 @@ public class AnnotationFile
     {
       ex.printStackTrace();
       System.out.println("Problem reading annotation file: " + ex);
+      if (nlinesread>0) {
+        System.out.println("Last read line "+nlinesread+": '"+lastread+"' (first 80 chars) ...");
+      }
       return false;
     }
     return false;
   }
-
+  long nlinesread=0;
+  String lastread="";
   public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
           throws Exception
   {
+    nlinesread = 0;
+    ArrayList<Object[]> combineAnnotation_calls = new ArrayList<Object[]>();
     boolean modified = false;
     String groupRef = null;
     Hashtable groupRefRows = new Hashtable();
@@ -631,6 +670,7 @@ public class AnnotationFile
       boolean jvAnnotationFile = false;
       while ((line = in.readLine()) != null)
       {
+        nlinesread++;lastread = new String(line);
         if (line.indexOf("#") == 0)
         {
           continue;
@@ -651,6 +691,7 @@ public class AnnotationFile
 
       while ((line = in.readLine()) != null)
       {
+        nlinesread++;lastread = new String(line);
         if (line.indexOf("#") == 0
                 || line.indexOf("JALVIEW_ANNOTATION") > -1
                 || line.length() == 0)
@@ -670,7 +711,8 @@ public class AnnotationFile
 
         else if (token.equalsIgnoreCase("COMBINE"))
         {
-          combineAnnotations(al, st);
+          // keep a record of current state and resolve groupRef at end
+          combineAnnotation_calls.add(new Object[] { st, refSeq, groupRef});
           modified = true;
           continue;
         }
@@ -885,7 +927,8 @@ public class AnnotationFile
         // and set modification flag
         modified = true;
       }
-      // Finally, resolve the groupRefs
+      // Resolve the groupRefs
+      Hashtable <String,SequenceGroup> groupRefLookup=new Hashtable<String,SequenceGroup>();
       Enumeration en = groupRefRows.keys();
 
       while (en.hasMoreElements())
@@ -909,6 +952,7 @@ public class AnnotationFile
             {
               matched = true;
               Vector rowset = (Vector) groupRefRows.get(groupRef);
+              groupRefLookup.put(groupRef,  theGroup);
               if (rowset != null && rowset.size() > 0)
               {
                 AlignmentAnnotation alan = null;
@@ -923,6 +967,20 @@ public class AnnotationFile
         }
         ((Vector) groupRefRows.get(groupRef)).removeAllElements();
       }
+      // finally, combine all the annotation rows within each context.
+      /**
+       * number of combine statements in this annotation file. Used to create new groups for combined annotation graphs without disturbing existing ones
+       */
+      int combinecount = 0;
+      for (Object[] _combine_args:combineAnnotation_calls) {
+        combineAnnotations(al, 
+                ++combinecount,
+                (StringTokenizer) _combine_args[0], // st
+                (SequenceI) _combine_args[1], // refSeq
+                (_combine_args[2]==null) ? null : groupRefLookup.get((String)_combine_args[2]) // the reference group, or null
+                );
+      }
+
     }
     return modified;
   }
@@ -1079,19 +1137,34 @@ public class AnnotationFile
     }
   }
 
-  void combineAnnotations(AlignmentI al, StringTokenizer st)
+  void combineAnnotations(AlignmentI al, int combineCount, StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef)
   {
-    int graphGroup = -1;
     String group = st.nextToken();
     // First make sure we are not overwriting the graphIndex
+    int graphGroup=0;
     if (al.getAlignmentAnnotation() != null)
     {
       for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
       {
-        if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
+        AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
+        
+        if (aa.graphGroup>graphGroup)
+        {
+          // try to number graphGroups in order of occurence.
+          graphGroup=aa.graphGroup+1;
+        }
+        if (aa.sequenceRef==seqRef && aa.groupRef==groupRef && aa.label.equalsIgnoreCase(group))
         {
-          graphGroup = al.getAlignmentAnnotation()[i].graphGroup + 1;
-          al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
+          if (aa.graphGroup>-1)
+          {
+            graphGroup = aa.graphGroup;
+          } else {
+            if (graphGroup <= combineCount)
+            {
+              graphGroup=combineCount+1;
+            }
+            aa.graphGroup = graphGroup;
+          }
           break;
         }
       }
@@ -1102,9 +1175,10 @@ public class AnnotationFile
         group = st.nextToken();
         for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
         {
-          if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
+          AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
+          if (aa.sequenceRef==seqRef && aa.groupRef==groupRef && aa.label.equalsIgnoreCase(group))
           {
-            al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
+            aa.graphGroup = graphGroup;
             break;
           }
         }

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 85ea8e0..eac7cf2 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -52,14 +52,16 @@ public class AppletFormatAdapter
    * that are writable by the application.
    */
   public static final String[] WRITABLE_EXTENSIONS = new String[]
-  { "fa,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
+  { "fa,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
+      "sto,stk" };
 
   /**
    * List of writable formats by the application. Order must correspond with the
    * WRITABLE_EXTENSIONS list of formats.
    */
   public static final String[] WRITABLE_FNAMES = new String[]
-  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview" };
+  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
+      "STH" };
 
   /**
    * List of readable format file extensions by application in order
@@ -455,7 +457,7 @@ public class AppletFormatAdapter
       }
       else if (format.equalsIgnoreCase("STH"))
       {
-        afile = new StockholmFile();
+        afile = new StockholmFile(alignment);
       }
       else if (format.equalsIgnoreCase("AMSA"))
       {
@@ -549,7 +551,6 @@ public class AppletFormatAdapter
           System.out
                   .println("Difference between free memory now and before is "
                           + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
-
         } catch (Exception e)
         {
           System.err.println("Exception when dealing with " + i

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 27b4944..ab5de61 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -328,9 +328,14 @@ public class FileLoader implements Runnable
 
             if (!protocol.equals(AppletFormatAdapter.PASTE))
               alignFrame.setFileName(file, format);
-
-            Desktop.addInternalFrame(alignFrame, title,
-                    AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+            if (raiseGUI)
+            {
+              // add the window to the GUI
+              // note - this actually should happen regardless of raiseGUI status in Jalview 3
+              // TODO: define 'virtual desktop' for benefit of headless scripts that perform queries to find the 'current working alignment'
+              Desktop.addInternalFrame(alignFrame, title,
+                      AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+            }
 
             try
             {

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index b0d3c8b..d730c9c 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -21,9 +21,13 @@
 package jalview.io;\r
 \r
 import jalview.datamodel.AlignmentAnnotation;\r
+import jalview.datamodel.AlignmentI;\r
 import jalview.datamodel.Annotation;\r
+import jalview.datamodel.DBRefEntry;\r
 import jalview.datamodel.Sequence;\r
+import jalview.datamodel.SequenceFeature;\r
 import jalview.datamodel.SequenceI;\r
+import jalview.util.Format;\r
 \r
 import java.io.BufferedReader;\r
 import java.io.FileReader;\r
@@ -31,6 +35,8 @@ import java.io.IOException;
 import java.util.ArrayList;\r
 import java.util.Enumeration;\r
 import java.util.Hashtable;\r
+import java.util.List;\r
+import java.util.StringTokenizer;\r
 import java.util.Vector;\r
 \r
 import com.stevesoft.pat.Regex;\r
@@ -50,6 +56,9 @@ import fr.orsay.lri.varna.models.rna.RNA;
  * into Jalview's local representation.\r
  * \r
  * @author bsb at sanger.ac.uk\r
+ * @author Natasha Shersnev (Dundee, UK) (Stockholm file writer)\r
+ * @author Lauren Lui (UCSC, USA) (RNA secondary structure annotation import as stockholm)\r
+ * @author Anne Menard (Paris, FR) (VARNA parsing of Stockholm file data)\r
  * @version 0.3 + jalview mods\r
  * \r
  */\r
@@ -57,6 +66,9 @@ public class StockholmFile extends AlignFile
 {\r
   // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");\r
   protected ArrayList<RNA> result;\r
+  StringBuffer out; // output buffer
+
+  AlignmentI al;
 \r
   public String id;\r
 \r
@@ -64,6 +76,14 @@ public class StockholmFile extends AlignFile
   {\r
   }\r
 \r
+  /**
+   * Creates a new StockholmFile object for output.
+   */
+  public StockholmFile(AlignmentI al)
+  {
+    this.al = al;
+  }
+
   public StockholmFile(String inFile, String type) throws IOException\r
   {\r
     super(inFile, type);\r
@@ -80,13 +100,9 @@ public class StockholmFile extends AlignFile
   }\r
 \r
   /**\r
-   * Parse a file in Stockholm format into Jalview's data model. The file has to\r
-   * be passed at construction time\r
-   * \r
-   * @throws IOException\r
-   *           If there is an error with the input file\r
+   * Parse a file in Stockholm format using VARNA\r
    */\r
-  public void parse() throws IOException\r
+  public void _parse_withVARNA(java.io.File inFile) throws IOException\r
   {\r
     FileReader fr = null;\r
     fr = new FileReader(inFile);\r
@@ -144,6 +160,588 @@ public class StockholmFile extends AlignFile
 \r
   }\r
 \r
+  \r
+  /**\r
+   * Parse a file in Stockholm format into Jalview's data model. The file has to\r
+   * be passed at construction time\r
+   * \r
+   * @throws IOException\r
+   *           If there is an error with the input file\r
+   */\r
+  public void parse() throws IOException\r
+  {\r
+    StringBuffer treeString = new StringBuffer();\r
+    String treeName = null;\r
+    // --------------- Variable Definitions -------------------\r
+    String line;\r
+    String version;\r
+    // String id;\r
+    Hashtable seqAnn = new Hashtable(); // Sequence related annotations\r
+    Hashtable seqs = new Hashtable();\r
+    Regex p, r, rend, s, x;\r
+\r
+    // Temporary line for processing RNA annotation\r
+    // String RNAannot = "";\r
+\r
+    // ------------------ Parsing File ----------------------\r
+    // First, we have to check that this file has STOCKHOLM format, i.e. the\r
+    // first line must match\r
+    r = new Regex("# STOCKHOLM ([\\d\\.]+)");\r
+    if (!r.search(nextLine()))\r
+    {\r
+      throw new IOException(\r
+              "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");\r
+    }\r
+    else\r
+    {\r
+      version = r.stringMatched(1);\r
+      // logger.debug("Stockholm version: " + version);\r
+    }\r
+\r
+    // We define some Regexes here that will be used regularily later\r
+    rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment\r
+    p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in\r
+    // id/from/to\r
+    s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype\r
+    r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line\r
+    x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence\r
+\r
+    // Convert all bracket types to parentheses (necessary for passing to VARNA)\r
+    Regex openparen = new Regex("(<|\\[)", "(");\r
+    Regex closeparen = new Regex("(>|\\])", ")");\r
+\r
+    // Detect if file is RNA by looking for bracket types\r
+    Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");\r
+\r
+    rend.optimize();\r
+    p.optimize();\r
+    s.optimize();\r
+    r.optimize();\r
+    x.optimize();\r
+    openparen.optimize();\r
+    closeparen.optimize();\r
+\r
+    while ((line = nextLine()) != null)\r
+    {\r
+      if (line.length() == 0)\r
+      {\r
+        continue;\r
+      }\r
+      if (rend.search(line))\r
+      {\r
+        // End of the alignment, pass stuff back\r
+        this.noSeqs = seqs.size();\r
+\r
+        String seqdb,dbsource = null;\r
+        Regex pf = new Regex("PF[0-9]{5}(.*)"); // Finds AC for Pfam\r
+        Regex rf = new Regex("RF[0-9]{5}(.*)"); // Finds AC for Rfam\r
+        if (getAlignmentProperty("AC") != null)\r
+        {\r
+          String dbType = getAlignmentProperty("AC").toString();\r
+          if (pf.search(dbType))\r
+          {\r
+            // PFAM Alignment - so references are typically from Uniprot\r
+            dbsource = "PFAM";\r
+          }\r
+          else if (rf.search(dbType))\r
+          {\r
+            dbsource = "RFAM";\r
+          }\r
+        }\r
+        // logger.debug("Number of sequences: " + this.noSeqs);\r
+        Enumeration accs = seqs.keys();\r
+        while (accs.hasMoreElements())\r
+        {\r
+          String acc = (String) accs.nextElement();\r
+          // logger.debug("Processing sequence " + acc);\r
+          String seq = (String) seqs.remove(acc);\r
+          if (maxLength < seq.length())\r
+          {\r
+            maxLength = seq.length();\r
+          }\r
+          int start = 1;\r
+          int end = -1;\r
+          String sid = acc;\r
+          /*\r
+           * Retrieve hash of annotations for this accession Associate\r
+           * Annotation with accession\r
+           */\r
+          Hashtable accAnnotations = null;\r
+\r
+          if (seqAnn != null && seqAnn.containsKey(acc))\r
+          {\r
+            accAnnotations = (Hashtable) seqAnn.remove(acc);\r
+            // TODO: add structures to sequence\r
+          }\r
+\r
+          // Split accession in id and from/to\r
+          if (p.search(acc))\r
+          {\r
+            sid = p.stringMatched(1);\r
+            start = Integer.parseInt(p.stringMatched(2));\r
+            end = Integer.parseInt(p.stringMatched(3));\r
+          }\r
+          // logger.debug(sid + ", " + start + ", " + end);\r
+\r
+          Sequence seqO = new Sequence(sid, seq, start, end);\r
+          // Add Description (if any)\r
+          if (accAnnotations != null && accAnnotations.containsKey("DE"))\r
+          {\r
+            String desc = (String) accAnnotations.get("DE");\r
+            seqO.setDescription((desc == null) ? "" : desc);\r
+          }\r
+\r
+          // Add DB References (if any)\r
+          if (accAnnotations != null && accAnnotations.containsKey("DR"))\r
+          {\r
+            String dbr = (String) accAnnotations.get("DR");\r
+            if (dbr != null && dbr.indexOf(";") > -1)\r
+            {\r
+              String src = dbr.substring(0, dbr.indexOf(";"));\r
+              String acn = dbr.substring(dbr.indexOf(";") + 1);\r
+              jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);\r
+            }\r
+          }\r
+\r
+          if (accAnnotations != null && accAnnotations.containsKey("AC"))\r
+          {\r
+            if (dbsource != null)\r
+            {\r
+              String dbr = (String) accAnnotations.get("AC");\r
+              if (dbr != null)\r
+              {\r
+                // we could get very clever here - but for now - just try to guess accession type from source of alignment plus structure of accession\r
+                guessDatabaseFor(seqO, dbr, dbsource);\r
+                \r
+              }\r
+            } \r
+            // else - do what ?  add the data anyway and prompt the user to specify what references these are ?\r
+          }\r
+\r
+          Hashtable features = null;\r
+          // We need to adjust the positions of all features to account for gaps\r
+          try\r
+          {\r
+            features = (Hashtable) accAnnotations.remove("features");\r
+          } catch (java.lang.NullPointerException e)\r
+          {\r
+            // loggerwarn("Getting Features for " + acc + ": " +\r
+            // e.getMessage());\r
+            // continue;\r
+          }\r
+          // if we have features\r
+          if (features != null)\r
+          {\r
+            int posmap[] = seqO.findPositionMap();\r
+            Enumeration i = features.keys();\r
+            while (i.hasMoreElements())\r
+            {\r
+              // TODO: parse out secondary structure annotation as annotation\r
+              // row\r
+              // TODO: parse out scores as annotation row\r
+              // TODO: map coding region to core jalview feature types\r
+              String type = i.nextElement().toString();\r
+              Hashtable content = (Hashtable) features.remove(type);\r
+\r
+              // add alignment annotation for this feature\r
+              String key = type2id(type);\r
+              if (key != null)\r
+              {\r
+                if (accAnnotations != null\r
+                        && accAnnotations.containsKey(key))\r
+                {\r
+                  Vector vv = (Vector) accAnnotations.get(key);\r
+                  for (int ii = 0; ii < vv.size(); ii++)\r
+                  {\r
+                    AlignmentAnnotation an = (AlignmentAnnotation) vv\r
+                            .elementAt(ii);\r
+                    seqO.addAlignmentAnnotation(an);\r
+                  }\r
+                }\r
+              }\r
+\r
+              Enumeration j = content.keys();\r
+              while (j.hasMoreElements())\r
+              {\r
+                String desc = j.nextElement().toString();\r
+                String ns = content.get(desc).toString();\r
+                char[] byChar = ns.toCharArray();\r
+                for (int k = 0; k < byChar.length; k++)\r
+                {\r
+                  char c = byChar[k];\r
+                  if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM\r
+                  // uses\r
+                  // '.'\r
+                  // for\r
+                  // feature\r
+                  // background\r
+                  {\r
+                    int new_pos = posmap[k]; // look up nearest seqeunce\r
+                    // position to this column\r
+                    SequenceFeature feat = new SequenceFeature(type, desc,\r
+                            new_pos, new_pos, 0f, null);\r
+\r
+                    seqO.addSequenceFeature(feat);\r
+                  }\r
+                }\r
+              }\r
+\r
+            }\r
+\r
+          }\r
+          // garbage collect\r
+\r
+          // logger.debug("Adding seq " + acc + " from " + start + " to " + end\r
+          // + ": " + seq);\r
+          this.seqs.addElement(seqO);\r
+        }\r
+        return; // finished parsing this segment of source\r
+      }\r
+      else if (!r.search(line))\r
+      {\r
+        // System.err.println("Found sequence line: " + line);\r
+\r
+        // Split sequence in sequence and accession parts\r
+        if (!x.search(line))\r
+        {\r
+          // logger.error("Could not parse sequence line: " + line);\r
+          throw new IOException("Could not parse sequence line: " + line);\r
+        }\r
+        String ns = (String) seqs.get(x.stringMatched(1));\r
+        if (ns == null)\r
+        {\r
+          ns = "";\r
+        }\r
+        ns += x.stringMatched(2);\r
+\r
+        seqs.put(x.stringMatched(1), ns);\r
+      }\r
+      else\r
+      {\r
+        String annType = r.stringMatched(1);\r
+        String annContent = r.stringMatched(2);\r
+\r
+        // System.err.println("type:" + annType + " content: " + annContent);\r
+\r
+        if (annType.equals("GF"))\r
+        {\r
+          /*\r
+           * Generic per-File annotation, free text Magic features: #=GF NH\r
+           * <tree in New Hampshire eXtended format> #=GF TN <Unique identifier\r
+           * for the next tree> Pfam descriptions: 7. DESCRIPTION OF FIELDS\r
+           * \r
+           * Compulsory fields: ------------------\r
+           * \r
+           * AC Accession number: Accession number in form PFxxxxx.version or\r
+           * PBxxxxxx. ID Identification: One word name for family. DE\r
+           * Definition: Short description of family. AU Author: Authors of the\r
+           * entry. SE Source of seed: The source suggesting the seed members\r
+           * belong to one family. GA Gathering method: Search threshold to\r
+           * build the full alignment. TC Trusted Cutoff: Lowest sequence score\r
+           * and domain score of match in the full alignment. NC Noise Cutoff:\r
+           * Highest sequence score and domain score of match not in full\r
+           * alignment. TP Type: Type of family -- presently Family, Domain,\r
+           * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM\r
+           * Alignment Method The order ls and fs hits are aligned to the model\r
+           * to build the full align. // End of alignment.\r
+           * \r
+           * Optional fields: ----------------\r
+           * \r
+           * DC Database Comment: Comment about database reference. DR Database\r
+           * Reference: Reference to external database. RC Reference Comment:\r
+           * Comment about literature reference. RN Reference Number: Reference\r
+           * Number. RM Reference Medline: Eight digit medline UI number. RT\r
+           * Reference Title: Reference Title. RA Reference Author: Reference\r
+           * Author RL Reference Location: Journal location. PI Previous\r
+           * identifier: Record of all previous ID lines. KW Keywords: Keywords.\r
+           * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.\r
+           * NL Location: Location of nested domains - sequence ID, start and\r
+           * end of insert.\r
+           * \r
+           * Obsolete fields: ----------- AL Alignment method of seed: The\r
+           * method used to align the seed members.\r
+           */\r
+          // Let's save the annotations, maybe we'll be able to do something\r
+          // with them later...\r
+          Regex an = new Regex("(\\w+)\\s*(.*)");\r
+          if (an.search(annContent))\r
+          {\r
+            if (an.stringMatched(1).equals("NH"))\r
+            {\r
+              treeString.append(an.stringMatched(2));\r
+            }\r
+            else if (an.stringMatched(1).equals("TN"))\r
+            {\r
+              if (treeString.length() > 0)\r
+              {\r
+                if (treeName == null)\r
+                {\r
+                  treeName = "Tree " + (getTreeCount() + 1);\r
+                }\r
+                addNewickTree(treeName, treeString.toString());\r
+              }\r
+              treeName = an.stringMatched(2);\r
+              treeString = new StringBuffer();\r
+            }\r
+            setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));\r
+          }\r
+        }\r
+        else if (annType.equals("GS"))\r
+        {\r
+          // Generic per-Sequence annotation, free text\r
+          /*\r
+           * Pfam uses these features: Feature Description ---------------------\r
+           * ----------- AC <accession> ACcession number DE <freetext>\r
+           * DEscription DR <db>; <accession>; Database Reference OS <organism>\r
+           * OrganiSm (species) OC <clade> Organism Classification (clade, etc.)\r
+           * LO <look> Look (Color, etc.)\r
+           */\r
+          if (s.search(annContent))\r
+          {\r
+            String acc = s.stringMatched(1);\r
+            String type = s.stringMatched(2);\r
+            String content = s.stringMatched(3);\r
+            // TODO: store DR in a vector.\r
+            // TODO: store AC according to generic file db annotation.\r
+            Hashtable ann;\r
+            if (seqAnn.containsKey(acc))\r
+            {\r
+              ann = (Hashtable) seqAnn.get(acc);\r
+            }\r
+            else\r
+            {\r
+              ann = new Hashtable();\r
+            }\r
+            ann.put(type, content);\r
+            seqAnn.put(acc, ann);\r
+          }\r
+          else\r
+          {\r
+            throw new IOException("Error parsing " + line);\r
+          }\r
+        }\r
+        else if (annType.equals("GC"))\r
+        {\r
+          // Generic per-Column annotation, exactly 1 char per column\r
+          // always need a label.\r
+          if (x.search(annContent))\r
+          {\r
+            // parse out and create alignment annotation directly.\r
+            parseAnnotationRow(annotations, x.stringMatched(1),\r
+                    x.stringMatched(2));\r
+          }\r
+        }\r
+        else if (annType.equals("GR"))\r
+        {\r
+          // Generic per-Sequence AND per-Column markup, exactly 1 char per\r
+          // column\r
+          /*\r
+           * Feature Description Markup letters ------- -----------\r
+           * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface\r
+           * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane\r
+           * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;\r
+           * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in\r
+           * or after) [0-2]\r
+           */\r
+          if (s.search(annContent))\r
+          {\r
+            String acc = s.stringMatched(1);\r
+            String type = s.stringMatched(2);\r
+            String seq = new String(s.stringMatched(3));\r
+            String description = null;\r
+            // Check for additional information about the current annotation\r
+            // We use a simple string tokenizer here for speed\r
+            StringTokenizer sep = new StringTokenizer(seq, " \t");\r
+            description = sep.nextToken();\r
+            if (sep.hasMoreTokens())\r
+            {\r
+              seq = sep.nextToken();\r
+            }\r
+            else\r
+            {\r
+              seq = description;\r
+              description = new String();\r
+            }\r
+            // sequence id with from-to fields\r
+\r
+            Hashtable ann;\r
+            // Get an object with all the annotations for this sequence\r
+            if (seqAnn.containsKey(acc))\r
+            {\r
+              // logger.debug("Found annotations for " + acc);\r
+              ann = (Hashtable) seqAnn.get(acc);\r
+            }\r
+            else\r
+            {\r
+              // logger.debug("Creating new annotations holder for " + acc);\r
+              ann = new Hashtable();\r
+              seqAnn.put(acc, ann);\r
+            }\r
+            // TODO test structure, call parseAnnotationRow with vector from\r
+            // hashtable for specific sequence\r
+            Hashtable features;\r
+            // Get an object with all the content for an annotation\r
+            if (ann.containsKey("features"))\r
+            {\r
+              // logger.debug("Found features for " + acc);\r
+              features = (Hashtable) ann.get("features");\r
+            }\r
+            else\r
+            {\r
+              // logger.debug("Creating new features holder for " + acc);\r
+              features = new Hashtable();\r
+              ann.put("features", features);\r
+            }\r
+\r
+            Hashtable content;\r
+            if (features.containsKey(this.id2type(type)))\r
+            {\r
+              // logger.debug("Found content for " + this.id2type(type));\r
+              content = (Hashtable) features.get(this.id2type(type));\r
+            }\r
+            else\r
+            {\r
+              // logger.debug("Creating new content holder for " +\r
+              // this.id2type(type));\r
+              content = new Hashtable();\r
+              features.put(this.id2type(type), content);\r
+            }\r
+            String ns = (String) content.get(description);\r
+            if (ns == null)\r
+            {\r
+              ns = "";\r
+            }\r
+            ns += seq;\r
+            content.put(description, ns);\r
+            Hashtable strucAnn;\r
+            if (seqAnn.containsKey(acc))\r
+            {\r
+              strucAnn = (Hashtable) seqAnn.get(acc);\r
+            }\r
+            else\r
+            {\r
+              strucAnn = new Hashtable();\r
+            }\r
+\r
+            Vector newStruc = new Vector();\r
+            parseAnnotationRow(newStruc, type, ns);\r
+            strucAnn.put(type, newStruc);\r
+            seqAnn.put(acc, strucAnn);\r
+          }\r
+          else\r
+          {\r
+            System.err\r
+                    .println("Warning - couldn't parse sequence annotation row line:\n"\r
+                            + line);\r
+            // throw new IOException("Error parsing " + line);\r
+          }\r
+        }\r
+        else\r
+        {\r
+          throw new IOException("Unknown annotation detected: " + annType\r
+                  + " " + annContent);\r
+        }\r
+      }\r
+    }\r
+    if (treeString.length() > 0)\r
+    {\r
+      if (treeName == null)\r
+      {\r
+        treeName = "Tree " + (1 + getTreeCount());\r
+      }\r
+      addNewickTree(treeName, treeString.toString());\r
+    }\r
+  }\r
+\r
+  /**\r
+   * Demangle an accession string and guess the originating sequence database for a given sequence\r
+   * @param seqO sequence to be annotated\r
+   * @param dbr Accession string for sequence\r
+   * @param dbsource source database for alignment (PFAM or RFAM)\r
+   */\r
+  private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)\r
+  {\r
+    DBRefEntry dbrf=null;\r
+    List<DBRefEntry> dbrs=new ArrayList<DBRefEntry>();\r
+    String seqdb="Unknown",sdbac=""+dbr;\r
+    int st=-1,en=-1,p;\r
+    if ((st=sdbac.indexOf("/"))>-1)\r
+    {\r
+      String num,range=sdbac.substring(st+1);\r
+      sdbac = sdbac.substring(0,st);\r
+      if ((p=range.indexOf("-"))>-1)\r
+      {\r
+        p++;\r
+        if (p<range.length())\r
+        {\r
+        num = range.substring(p).trim();\r
+        try {\r
+          en = Integer.parseInt(num);\r
+        } catch (NumberFormatException x)\r
+        {\r
+          // could warn here that index is invalid\r
+          en = -1;\r
+        }\r
+        }\r
+      } else {\r
+        p=range.length();\r
+      }\r
+      num=range.substring(0,p).trim();\r
+      try {\r
+        st = Integer.parseInt(num);\r
+      } catch (NumberFormatException x)\r
+      {\r
+        // could warn here that index is invalid\r
+        st = -1;\r
+      }\r
+    }\r
+    if (dbsource.equals("PFAM")) {\r
+      seqdb = "UNIPROT";\r
+      if (sdbac.indexOf(".")>-1)\r
+      {\r
+        // strip of last subdomain\r
+        sdbac = sdbac.substring(0,sdbac.indexOf("."));\r
+        dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource, sdbac);\r
+        if (dbrf!=null)\r
+        {\r
+          dbrs.add(dbrf);\r
+        }\r
+      }\r
+      dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource, dbr);\r
+      if (dbr!=null)\r
+      {\r
+        dbrs.add(dbrf);\r
+      }\r
+    } else {\r
+      seqdb = "EMBL"; // total guess - could be ENA, or something else these days\r
+      if (sdbac.indexOf(".")>-1)\r
+      {\r
+        // strip off last subdomain\r
+        sdbac = sdbac.substring(0,sdbac.indexOf("."));\r
+        dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource, sdbac);\r
+        if (dbrf!=null)\r
+        {\r
+          dbrs.add(dbrf);\r
+        }\r
+      }\r
+      \r
+      dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource, dbr);\r
+      if (dbrf!=null)\r
+      {\r
+        dbrs.add(dbrf);\r
+      }\r
+    }\r
+    if (st!=-1 && en!=-1)\r
+    {\r
+      for (DBRefEntry d:dbrs)\r
+      {\r
+        jalview.util.MapList mp = new jalview.util.MapList(new int[] { seqO.getStart(),seqO.getEnd()},new int[] { st,en},1,1);\r
+        jalview.datamodel.Mapping mping = new jalview.datamodel.Mapping(mp);\r
+        d.setMap(mping);\r
+      }\r
+    }\r
+  }\r
+  \r
   protected static AlignmentAnnotation parseAnnotationRow(\r
           Vector annotation, String label, String annots)\r
   {\r
@@ -160,8 +758,12 @@ public class StockholmFile extends AlignFile
     convert2 = closeparen.replaceAll(convert1);\r
     annots = convert2;\r
 \r
-    String type = (label.indexOf("_cons") == label.length() - 5) ? label\r
+    String type = label;
+    if (label.contains("_cons"))
+    {
+      type = (label.indexOf("_cons") == label.length() - 5) ? label
             .substring(0, label.length() - 5) : label;\r
+    }
     boolean ss = false;\r
     type = id2type(type);\r
     if (type.equals("secondary structure"))\r
@@ -228,14 +830,211 @@ public class StockholmFile extends AlignFile
     return annot;\r
   }\r
 \r
-  public static String print(SequenceI[] s)\r
+  public String print(SequenceI[] s)
+  {
+    // find max length of id
+    int max = 0;
+    int maxid = 0;
+    int in = 0;
+    Hashtable dataRef = null;
+    while ((in < s.length) && (s[in] != null))
+    {
+      String tmp = printId(s[in]);
+      if (s[in].getSequence().length > max)
+      {
+        max = s[in].getSequence().length;
+      }
+
+      if (tmp.length() > maxid)
+      {
+        maxid = tmp.length();
+      }
+      if (s[in].getDBRef() != null)
+      {
+        for (int idb = 0; idb < s[in].getDBRef().length; idb++)
+        {
+          if (dataRef == null)
+            dataRef = new Hashtable();
+
+          String datAs1 = s[in].getDBRef()[idb].getSource().toString()
+                  + " ; "
+                  + s[in].getDBRef()[idb].getAccessionId().toString();
+          dataRef.put(tmp, datAs1);
+        }
+      }
+      in++;
+    }
+    maxid += 9;
+    int i = 0;
+
+    // output database type
+    if (al.getProperties() != null)
+    {
+      if (!al.getProperties().isEmpty())
+      {
+        Enumeration key = al.getProperties().keys();
+        Enumeration val = al.getProperties().elements();
+        while (key.hasMoreElements())
+        {
+          out.append("#=GF " + key.nextElement() + " " + val.nextElement());
+          out.append(newline);
+        }
+      }
+    }
+
+    // output database accessions
+    if (dataRef != null)
+    {
+      Enumeration en = dataRef.keys();
+      while (en.hasMoreElements())
+      {
+        Object idd = en.nextElement();
+        String type = (String) dataRef.remove(idd);
+        out.append(new Format("%-" + (maxid - 2) + "s").form("#=GS "
+                + idd.toString() + " "));
+        if (type.contains("PFAM") || type.contains("RFAM"))
+        {
+
+          out.append(" AC " + type.substring(type.indexOf(";") + 1));
+        }
+        else
+        {
+          out.append(" DR " + type + " ");
+        }
+        out.append(newline);
+      }
+    }
+
+    // output annotations
+    while (i < s.length && s[i] != null)
+    {
+      if (s[i].getDatasetSequence() != null)
+      {
+        SequenceI ds = s[i].getDatasetSequence();
+        AlignmentAnnotation[] alAnot;
+        Annotation[] ann;
+        Annotation annot;
+        alAnot = s[i].getAnnotation();
+        String feature = "";
+        if (alAnot != null)
+        {
+          for (int j = 0; j < alAnot.length; j++)
+          {
+            if (ds.getSequenceFeatures() != null)
+            {
+              feature = ds.getSequenceFeatures()[0].type;
+            }
+            String key = type2id(feature);
+
+            if (key == null)
+              continue;
+
+            // out.append("#=GR ");
+            out.append(new Format("%-" + maxid + "s").form("#=GR "
+                    + printId(s[i]) + " " + key + " "));
+            ann = alAnot[j].annotations;
+            String seq = "";
+            for (int k = 0; k < ann.length; k++)
+            {
+              annot = ann[k];
+              String ch = (annot == null) ? Character.toString(s[i]
+                      .getCharAt(k)) : annot.displayCharacter;
+              if (ch.length() == 0)
+              {
+                if (key.equals("SS"))
+                {
+                  char ll = annot.secondaryStructure;
+                  seq = (Character.toString(ll).equals(" ")) ? seq + "C"
+                          : seq + ll;
+                }
+                else
+                {
+                  seq += ".";
+                }
+              }
+              else if (ch.length() == 1)
+              {
+                seq += ch;
+              }
+              else if (ch.length() > 1)
+              {
+                seq += ch.charAt(1);
+              }
+            }
+            out.append(seq);
+            out.append(newline);
+          }
+        }
+      }
+
+      out.append(new Format("%-" + maxid + "s").form(printId(s[i]) + " "));
+      out.append(s[i].getSequenceAsString());
+      out.append(newline);
+      i++;
+    }
+
+    // alignment annotation
+    AlignmentAnnotation aa;
+    if (al.getAlignmentAnnotation() != null)
+    {
+      for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++)
+      {
+        aa = al.getAlignmentAnnotation()[ia];
+        if (aa.autoCalculated || !aa.visible)
+        {
+          continue;
+        }
+        String seq = "";
+        String label;
+
+        if (aa.label.equals("seq"))
+          label = "seq_cons";
+        else
+          label = type2id(aa.label.toLowerCase()) + "_cons";
+
+        if (label == null)
+          label = aa.label;
+
+        out.append(new Format("%-" + maxid + "s").form("#=GC " + label
+                + " "));
+        for (int j = 0; j < aa.annotations.length; j++)
+        {
+          String ch = (aa.annotations[j] == null) ? "-"
+                  : aa.annotations[j].displayCharacter;
+          if (ch.length() == 0)
+          {
+            char ll = aa.annotations[j].secondaryStructure;
+            if (Character.toString(ll).equals(" "))
+              seq += "C";
+            else
+              seq += ll;
+          }
+          else if (ch.length() == 1)
+          {
+            seq += ch;
+          }
+          else if (ch.length() > 1)
   {\r
-    return "not yet implemented";\r
+            seq += ch.charAt(1);
+          }
+        }
+        out.append(seq);
+        out.append(newline);
+      }
+    }
+    return out.toString();
   }\r
 \r
   public String print()\r
   {\r
-    return print(getSeqsAsArray());\r
+    out = new StringBuffer();
+    out.append("# STOCKHOLM 1.0");
+    out.append(newline);
+    print(getSeqsAsArray());
+
+    out.append("//");
+    out.append(newline);
+    return out.toString();
   }\r
 \r
   private static Hashtable typeIds = null;\r
@@ -273,6 +1072,28 @@ public class StockholmFile extends AlignFile
             + id);\r
     return id;\r
   }\r
+  \r
+  protected static String type2id(String type)\r
+  {\r
+    String key = null;\r
+    Enumeration e = typeIds.keys();\r
+    while (e.hasMoreElements())\r
+    {\r
+      Object ll = e.nextElement();\r
+      if (typeIds.get(ll).toString().equals(type))\r
+      {\r
+        key = (String) ll;\r
+        break;\r
+      }\r
+    }\r
+    if (key != null)\r
+    {\r
+      return (String) key;\r
+    }\r
+    System.err.println("Warning : Unknown Stockholm annotation type: "\r
+            + type);\r
+    return key;\r
+  }\r
   /**\r
    * make a friendly ID string.\r
    * \r

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 65f65bb..23726df 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -35,16 +35,29 @@ import java.awt.Image;
 import java.awt.font.LineMetrics;
 import java.awt.geom.AffineTransform;
 import java.awt.image.ImageObserver;
+import java.util.BitSet;
 import java.util.Hashtable;
 
 import com.stevesoft.pat.Regex;
 
 public class AnnotationRenderer
 {
+  /**
+   * flag indicating if timing and redraw parameter info should be output
+   */
+  private final boolean debugRedraw;
 
   public AnnotationRenderer()
   {
-    // TODO Auto-generated constructor stub
+    this(false);
+  }
+  /**
+   * Create a new annotation Renderer
+   * @param debugRedraw flag indicating if timing and redraw parameter info should be output
+   */
+  public AnnotationRenderer(boolean debugRedraw)
+  {
+    this.debugRedraw=debugRedraw;
   }
 
   public void drawStemAnnot(Graphics g, Annotation[] row_annotations,
@@ -143,6 +156,22 @@ public class AnnotationRenderer
    * width of image to render in panel
    */
   private int imgWidth;
+  /**
+   * offset to beginning of visible area
+   */
+  private int sOffset;
+  /**
+   * offset to end of visible area
+   */
+  private int visHeight;
+  /**
+   * indicate if the renderer should only render the visible portion of the annotation given the current view settings
+   */
+  private boolean useClip=true;
+  /**
+   * master flag indicating if renderer should ever try to clip. not enabled for jalview 2.8.1 
+   */
+  private boolean canClip=false;
 
   
   public void drawNotCanonicalAnnot(Graphics g, Color nonCanColor, Annotation[] row_annotations,
@@ -212,6 +241,22 @@ public class AnnotationRenderer
     annotationPanel = annotPanel;
     fadedImage = annotPanel.getFadedImage();
     imgWidth = annotPanel.getFadedImageWidth();
+    // visible area for rendering
+    int[] bounds=annotPanel.getVisibleVRange();
+    if (bounds!=null)
+    {
+      sOffset = bounds[0];
+      visHeight = bounds[1];
+      if (visHeight==0)
+      {
+        useClip=false;
+      } else {
+        useClip=canClip;
+      }
+    } else {
+      useClip=false;
+    }
+
     updateFromAlignViewport(av);
   }
 
@@ -311,6 +356,7 @@ public class AnnotationRenderer
           AlignViewportI av, Graphics g, int activeRow, int startRes,
           int endRes)
   {
+    long stime=System.currentTimeMillis();
     boolean usedFaded = false;
     // NOTES:
     // AnnotationPanel needs to implement: ImageObserver, access to
@@ -333,12 +379,16 @@ public class AnnotationRenderer
     boolean centreColLabels, centreColLabelsDef = av
             .getCentreColumnLabels();
     boolean scaleColLabel = false;
-    boolean[] graphGroupDrawn = new boolean[aa.length];
+
+    BitSet graphGroupDrawn = new BitSet();
     int charOffset = 0; // offset for a label
     float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
     // column.
     Font ofont = g.getFont();
     // \u03B2 \u03B1
+    // debug ints
+    int yfrom=0,f_i=0,yto=0,f_to=0;
+    boolean clipst=false,clipend=false;
     for (int i = 0; i < aa.length; i++)
     {
       AlignmentAnnotation row = aa[i];
@@ -352,10 +402,20 @@ public class AnnotationRenderer
       scaleColLabel = row.scaleColLabel;
       lastSS = ' ';
       lastSSX = 0;
+      
+      if (!useClip || ((y-charHeight)<visHeight && (y+row.height+charHeight*2)>=sOffset)) 
+      {// if_in_visible_region
+        if (!clipst)
+        {
+          clipst=true;
+          yfrom=y;
+          f_i=i;
+        }
+        yto = y;
+        f_to=i;
       if (row.graph > 0)
       {
-        if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup])
-        {
+        if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup)) {
           continue;
         }
 
@@ -1027,8 +1087,9 @@ public class AnnotationRenderer
       {
         if (row.graph == AlignmentAnnotation.LINE_GRAPH)
         {
-          if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup])
+          if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
           {
+            // TODO: JAL-1291 revise rendering model so the graphGroup map is computed efficiently for all visible labels
             float groupmax = -999999, groupmin = 9999999;
             for (int gg = 0; gg < aa.length; gg++)
             {
@@ -1060,7 +1121,7 @@ public class AnnotationRenderer
               }
             }
 
-            graphGroupDrawn[row.graphGroup] = true;
+            graphGroupDrawn.set(row.graphGroup);
           }
           else
           {
@@ -1074,7 +1135,12 @@ public class AnnotationRenderer
                   row.graphMin, row.graphMax, y);
         }
       }
-
+    } else {
+      if (clipst && !clipend)
+      {
+        clipend = true;
+      }
+    }// end if_in_visible_region
       if (row.graph > 0 && row.hasText)
       {
         y += charHeight;
@@ -1085,6 +1151,27 @@ public class AnnotationRenderer
         y += aa[i].height;
       }
     }
+    if (debugRedraw)
+    {
+      if (canClip)
+      {
+        if (clipst)
+        {
+          System.err.println("Start clip at : " + yfrom + " (index " + f_i
+                  + ")");
+        }
+        if (clipend)
+        {
+          System.err.println("End clip at : " + yto + " (index " + f_to
+                  + ")");
+        }
+      }
+      ;
+      System.err.println("Annotation Rendering time:"
+              + (System.currentTimeMillis() - stime));
+    }
+    ;
+
     return !usedFaded;
   }
 

diff --git a/src/jalview/renderer/AwtRenderPanelI.java b/src/jalview/renderer/AwtRenderPanelI.java
index 70bbc7b..e73a673 100644 (file)
--- a/src/jalview/renderer/AwtRenderPanelI.java
+++ b/src/jalview/renderer/AwtRenderPanelI.java
@@ -41,4 +41,10 @@ public interface AwtRenderPanelI extends ImageObserver
    */
   int getFadedImageWidth();
 
+  /**
+   * height of visible area on to the image - used to draw only what is visible.
+   * @return [start, end of visible region]
+   */
+  int[] getVisibleVRange();
+
 }

diff --git a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
index 55d32f5..f5021e6 100644 (file)
--- a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
+++ b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
@@ -201,7 +201,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
             }
             else
             {
-              System.err.println("FAILED TO CANCELL AACon job: " + rslt);
+              System.err.println("FAILED TO CANCEL AACon job: " + rslt);
             }
 
           } catch (Exception x)

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
new file mode 100644 (file)
index 0000000..30f61d7
--- /dev/null
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -0,0 +1,91 @@
+package jalview.io;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import jalview.datamodel.AlignmentI;
+
+import java.io.File;
+
+import org.junit.Test;
+
+public class AnnotationFileIOTest
+{
+
+  static String TestFiles[][] = {{ "Test example annotation import/export","examples/uniref50.fa", "examples/testdata/example_annot_file.jva" }
+          ,{"Test multiple combine annotation statements import/export","examples/uniref50.fa", "examples/testdata/test_combine_annot.jva"}
+          ,{"Test multiple combine annotation statements with sequence_ref import/export","examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva"}};
+
+  @Test
+  public void exampleAnnotationFileIO() throws Exception
+  {
+    for (String[] testPair:TestFiles)
+    {
+      testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(testPair[2]));
+    }
+  }
+
+  public static AlignmentI readAlignmentFile(File f)
+  {
+    System.out.println("Reading file: " + f);
+    String ff = f.getPath();
+    try
+    {
+      FormatAdapter rf = new FormatAdapter();
+
+      AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
+              new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
+      
+      // make sure dataset is initialised ? not sure about this
+      for (int i = 0; i < al.getSequencesArray().length; ++i)
+      {
+        al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i).createDatasetSequence());
+      }
+      assertNotNull("Couldn't read supplied alignment data.", al);
+      return al;
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    fail("Couln't read the alignment in file '"+f.toString()+"'");
+    return null;
+  }
+  /**
+   * test alignment data in given file can be imported, exported and reimported
+   * with no dataloss
+   * 
+   * @param f
+   *          - source datafile (IdentifyFile.identify() should work with it)
+   * @param ioformat
+   *          - label for IO class used to write and read back in the data from
+   *          f
+   */
+  public static void testAnnotationFileIO(String testname, File f, File annotFile)
+  {
+    System.out.println("Test: "+testname+"\nReading annotation file '"+annotFile+"' onto : " + f);
+    String af = annotFile.getPath();
+    try
+    {
+      AlignmentI al = readAlignmentFile(f);
+      
+      assertTrue("Test "+testname+"\nAlignment was not annotated - annotation file not imported.",new AnnotationFile().readAnnotationFile(al, af, FormatAdapter.FILE));
+      
+      String anfileout = new AnnotationFile().printAnnotations(al.getAlignmentAnnotation(), al.getGroups(), al.getProperties());
+      assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Null string",anfileout!=null);
+      assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Empty string",anfileout.length()>"JALVIEW_ANNOTATION".length());
+
+      System.out.println("Output annotation file:\n"+anfileout+"\n<<EOF\n");
+      
+      AlignmentI al_new = readAlignmentFile(f);
+      assertTrue("Test "+testname+"\nregenerated annotation file did not annotate alignment.",new AnnotationFile().readAnnotationFile(al_new, anfileout, FormatAdapter.PASTE));
+      
+      // test for consistency in io
+      StockholmFileTest.testAlignmentEquivalence(al, al_new);
+      return;
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    fail("Test "+testname+"\nCouldn't complete Annotation file roundtrip input/output/input test for '"+annotFile+"'.");
+  }
+}

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
new file mode 100644 (file)
index 0000000..a0c9336
--- /dev/null
+++ b/test/jalview/io/StockholmFileTest.java
@@ -0,0 +1,304 @@
+package jalview.io;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+
+import java.io.File;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.junit.Test;
+
+public class StockholmFileTest
+{
+
+  static String PfamFile = "examples/PF00111_seed.stk",
+          RfamFile = "examples/RF00031_folded.stk";
+
+  @Test
+  public void pfamFileIO() throws Exception
+  {
+    testFileIOwithFormat(new File(PfamFile), "STH");
+  }
+  @Test
+  public void pfamFileDataExtraction() throws Exception
+  {  AppletFormatAdapter af = new AppletFormatAdapter();
+    AlignmentI al = af.readFile(PfamFile, af.FILE,
+            new IdentifyFile().Identify(PfamFile, af.FILE));
+    int numpdb = 0;
+    for (SequenceI sq : al.getSequences())
+    {
+      if (sq.getPDBId() != null)
+      {
+        numpdb += sq.getPDBId().size();
+      }
+    }
+    assertTrue(
+            "PF00111 seed alignment has at least 1 PDB file, but the reader found none.",
+            numpdb > 0);
+  }
+
+  @Test
+  public void rfamFileIO() throws Exception
+  {
+    testFileIOwithFormat(new File(RfamFile), "STH");
+  }
+
+  /**
+   * test alignment data in given file can be imported, exported and reimported
+   * with no dataloss
+   * 
+   * @param f
+   *          - source datafile (IdentifyFile.identify() should work with it)
+   * @param ioformat
+   *          - label for IO class used to write and read back in the data from
+   *          f
+   */
+  public static void testFileIOwithFormat(File f, String ioformat)
+  {
+    System.out.println("Reading file: " + f);
+    String ff = f.getPath();
+    try
+    {
+      AppletFormatAdapter rf = new AppletFormatAdapter();
+
+      Alignment al = rf.readFile(ff, AppletFormatAdapter.FILE,
+              new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
+
+      assertNotNull("Couldn't read supplied alignment data.", al);
+
+      // make sure dataset is initialised ? not sure about this
+      for (int i = 0; i < al.getSequencesArray().length; ++i)
+      {
+        al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i));
+      }
+      String outputfile = rf.formatSequences(ioformat, al, true);
+      System.out.println("Output file in '"+ioformat+"':\n"+outputfile+"\n<<EOF\n");
+      // test for consistency in io
+      Alignment al_input = new AppletFormatAdapter().readFile(outputfile,
+              AppletFormatAdapter.PASTE, ioformat);
+      assertNotNull("Couldn't parse reimported alignment data.", al_input);
+
+      String identifyoutput = new IdentifyFile().Identify(outputfile,
+              AppletFormatAdapter.PASTE);
+      assertNotNull("Identify routine failed for outputformat " + ioformat,
+              identifyoutput);
+      assertTrue(
+              "Identify routine could not recognise output generated by '"
+                      + ioformat + "' writer",
+              ioformat.equals(identifyoutput));
+      testAlignmentEquivalence(al, al_input);
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+      assertTrue("Couln't format the alignment for output file.", false);
+    }
+  }
+
+  /**
+   * assert alignment equivalence
+   * 
+   * @param al
+   *          'original'
+   * @param al_input
+   *          'secondary' or generated alignment from some datapreserving
+   *          transformation
+   */
+  public static void testAlignmentEquivalence(AlignmentI al,
+          AlignmentI al_input)
+  {
+    assertNotNull("Original alignment was null", al);
+    assertNotNull("Generated alignment was null", al_input);
+
+    assertTrue(
+            "Alignment dimension mismatch: originl contains "
+                    + al.getHeight() + " and generated has "
+                    + al_input.getHeight() + " sequences; original has "
+                    + al.getWidth() + " and generated has "
+                    + al_input.getWidth() + " columns.",
+            al.getHeight() == al_input.getHeight()
+                    && al.getWidth() == al_input.getWidth());
+
+    // check Alignment annotation
+    AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation();
+
+    // note - at moment we do not distinguish between alignment without any
+    // annotation rows and alignment with no annotation row vector
+    // we might want to revise this in future
+    int aa_new_size = (aa_new == null ? 0 : aa_new.length), aa_original_size = (aa_original == null ? 0
+            : aa_original.length);
+    Map<Integer,java.util.BitSet> orig_groups=new HashMap<Integer,java.util.BitSet>(),new_groups=new HashMap<Integer,java.util.BitSet>();
+
+    if (aa_new != null && aa_original != null)
+    {
+      for (int i = 0; i < aa_original.length; i++)
+      {
+        if (aa_new.length>i) {
+          assertTrue("Different alignment annotation at position "+i,
+                equalss(aa_original[i], aa_new[i]));
+          // compare graphGroup or graph properties - needed to verify JAL-1299
+          assertTrue("Graph type not identical.",aa_original[i].graph==aa_new[i].graph);
+          assertTrue("Visibility not identical.", aa_original[i].visible==aa_new[i].visible);
+          // graphGroup may differ, but pattern should be the same
+          Integer o_ggrp=new Integer(aa_original[i].graphGroup+2),n_ggrp=new Integer(aa_new[i].graphGroup+2);
+          BitSet orig_g=orig_groups.get(o_ggrp),new_g=new_groups.get(n_ggrp);
+          if (orig_g==null) {
+            orig_groups.put(o_ggrp,orig_g= new BitSet());
+          }
+          if (new_g==null) {
+            new_groups.put(n_ggrp, new_g=new BitSet());
+          }
+          assertTrue("Graph Group pattern differs at annotation "+i, orig_g.equals(new_g));
+          orig_g.set(i); new_g.set(i);
+        } else {
+          System.err.println("No matching annotation row for "+aa_original[i].toString());
+        }
+      }
+    }
+    assertTrue(
+            "Generated and imported alignment have different annotation sets ("
+                    + aa_new_size + " != " + aa_original_size + ")",
+            aa_new_size == aa_original_size);
+
+    // check sequences, annotation and features
+    SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
+    seq_original = al.getSequencesArray();
+    SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length];
+    seq_new = al_input.getSequencesArray();
+    SequenceFeature[] sequenceFeatures_original, sequenceFeatures_new;
+    AlignmentAnnotation annot_original, annot_new;
+    //
+    for (int i = 0; i < al.getSequencesArray().length; i++)
+    {
+      String name = seq_original[i].getName();
+      int start = seq_original[i].getStart();
+      int end = seq_original[i].getEnd();
+      System.out.println("Check sequence: " + name + "/" + start + "-"
+              + end);
+
+      // search equal sequence
+      for (int in = 0; in < al_input.getSequencesArray().length; in++)
+      {
+        if (name.equals(seq_new[in].getName())
+                && start == seq_new[in].getStart()
+                && end == seq_new[in].getEnd())
+        {
+          String ss_original = seq_original[i].getSequenceAsString();
+          String ss_new = seq_new[in].getSequenceAsString();
+          assertTrue("The sequences " + name + "/" + start + "-" + end
+                  + " are not equal", ss_original.equals(ss_new));
+
+          assertTrue(
+                  "Sequence Features were not equivalent",
+                  (seq_original[i].getSequenceFeatures() == null && seq_new[in]
+                          .getSequenceFeatures() == null)
+                          || (seq_original[i].getSequenceFeatures() != null && seq_new[in]
+                                  .getSequenceFeatures() != null));
+          // compare sequence features
+          if (seq_original[i].getSequenceFeatures() != null
+                  && seq_new[in].getSequenceFeatures() != null)
+          {
+            System.out.println("There are feature!!!");
+            sequenceFeatures_original = new SequenceFeature[seq_original[i]
+                    .getSequenceFeatures().length];
+            sequenceFeatures_original = seq_original[i]
+                    .getSequenceFeatures();
+            sequenceFeatures_new = new SequenceFeature[seq_new[in]
+                    .getSequenceFeatures().length];
+            sequenceFeatures_new = seq_new[in].getSequenceFeatures();
+
+            assertTrue("different number of features", seq_original[i]
+                    .getSequenceFeatures().length == seq_new[in]
+                    .getSequenceFeatures().length);
+
+            for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++)
+            {
+              assertTrue("Different features",
+                      sequenceFeatures_original[feat]
+                              .equals(sequenceFeatures_new[feat]));
+            }
+          }
+          // compare alignment annotation
+          if (al.getSequenceAt(i).getAnnotation() != null
+                  && al_input.getSequenceAt(in).getAnnotation() != null)
+          {
+            for (int j = 0; j < al.getSequenceAt(i).getAnnotation().length; j++)
+            {
+              if (al.getSequenceAt(i).getAnnotation()[j] != null
+                      && al_input.getSequenceAt(in).getAnnotation()[j] != null)
+              {
+                annot_original = al.getSequenceAt(i).getAnnotation()[j];
+                annot_new = al_input.getSequenceAt(in).getAnnotation()[j];
+                assertTrue("Different annotation elements",
+                        equalss(annot_original, annot_new));
+              }
+            }
+          }
+          else if (al.getSequenceAt(i).getAnnotation() == null
+                  && al_input.getSequenceAt(in).getAnnotation() == null)
+          {
+            System.out.println("No annotations");
+          }
+          else if (al.getSequenceAt(i).getAnnotation() != null
+                  && al_input.getSequenceAt(in).getAnnotation() == null)
+          {
+            assertTrue("Annotations differed between sequences ("
+                    + al.getSequenceAt(i).getName() + ") and ("
+                    + al_input.getSequenceAt(i).getName() + ")", false);
+          }
+          break;
+        }
+      }
+    }
+  }
+
+  /*
+   * compare annotations
+   */
+  private static boolean equalss(AlignmentAnnotation annot_or,
+          AlignmentAnnotation annot_new)
+  {
+    if (annot_or.annotations.length != annot_new.annotations.length)
+    {
+      System.err.println("Different lengths for annotation row elements: "+annot_or.annotations.length +"!="+ annot_new.annotations.length);
+      return false;
+    }
+    for (int i = 0; i < annot_or.annotations.length; i++)
+    {
+      Annotation an_or=annot_or.annotations[i],an_new=annot_new.annotations[i];
+      if (an_or != null
+              && an_new!= null)
+      {
+        if (!an_or.displayCharacter.trim()
+                .equals(an_new.displayCharacter.trim())
+                || !(""+an_or.secondaryStructure).trim().equals((""+an_new.secondaryStructure).trim())
+                || (an_or.description != an_new.description && (an_or.description == null
+                        || an_new.description == null || !an_or.description
+                          .equals(an_new.description))))
+        {
+          System.err.println("Annotation Element Mismatch\nElement "+i+" in original: "+annot_or.annotations[i].toString()+"\nElement "+i+" in new: "+annot_new.annotations[i].toString());
+          return false;
+        }
+      }
+      else if (annot_or.annotations[i] == null
+              && annot_new.annotations[i] == null)
+      {
+        continue;
+      }
+      else
+      {
+        System.err.println("Annotation Element Mismatch\nElement "+i+" in original: "+(annot_or.annotations[i]==null ? "is null" : annot_or.annotations[i].toString())+"\nElement "+i+" in new: "+(annot_new.annotations[i] == null ? "is null" : annot_new.annotations[i].toString()));
+        return false;
+      }
+    }
+    return true;
+  }
+}

diff --git a/test/jalview/ws/gui/Jws2ParamView.java b/test/jalview/ws/gui/Jws2ParamView.java
index b43ada2..2d40dd4 100644 (file)
--- a/test/jalview/ws/gui/Jws2ParamView.java
+++ b/test/jalview/ws/gui/Jws2ParamView.java
@@ -17,8 +17,9 @@
  */
 package jalview.ws.gui;
 
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.*;
 import jalview.gui.WsJobParameters;
+import jalview.ws.jabaws.JalviewJabawsTestUtils;
 import jalview.ws.jws2.JabaPreset;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
@@ -29,11 +30,11 @@ import java.awt.event.WindowListener;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
-import java.util.Vector;
 
 import javax.swing.JFrame;
 import javax.swing.JPanel;
 
+import org.junit.BeforeClass;
 import org.junit.Test;
 
 import compbio.metadata.Option;
@@ -44,12 +45,6 @@ import compbio.metadata.PresetManager;
 public class Jws2ParamView
 {
   /**
-   * test servers
-   */
-  public static String[] serviceUrls = new String[]
-  { "http://localhost:8080/jabaws" };
-
-  /**
    * which services to test
    */
   public static List<String> serviceTests = new ArrayList<String>();
@@ -63,33 +58,16 @@ public class Jws2ParamView
     serviceTests.add("AAConWS".toLowerCase());
   }
 
+  public static Jws2Discoverer disc=null;
+  @BeforeClass
+  public static void setUpBeforeClass() throws Exception
+  {
+    disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
+    
+  }
   @Test
   public void testJws2Gui()
   {
-    jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
-            .getDiscoverer();
-    int p = 0;
-    String svcurls="";
-    Vector<String> services = new Vector<String>();
-    for (String url : serviceUrls)
-    {
-      svcurls+=url+"; ";
-      services.add(url);
-    }
-    ;
-    Jws2Discoverer.setServiceUrls(services);
-
-    try
-    {
-      disc.run();
-    } catch (Exception e)
-    {
-      System.err.println("Aborting. Problem discovering services. Tried "+svcurls);
-      e.printStackTrace();
-      return;
-    }
-    assertTrue("Failed to discover any services at ",
-            disc.getServices().size() > 0);
     Jws2Instance lastserv = null;
     Iterator<String> presetEnum = presetTests.iterator();
     for (Jws2Instance service : disc.getServices())

diff --git a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
new file mode 100644 (file)
index 0000000..fa19d00
--- /dev/null
+++ b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
@@ -0,0 +1,144 @@
+package jalview.ws.jabaws;
+
+import static org.junit.Assert.*;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.io.AnnotationFile;
+import jalview.io.FormatAdapter;
+import jalview.io.StockholmFileTest;
+import jalview.ws.jws2.AADisorderClient;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+public class DisorderAnnotExportImport
+{
+  public static String testseqs = "examples/uniref50.fa";
+
+  public static Jws2Discoverer disc;
+
+  public static List<Jws2Instance> iupreds;
+
+  jalview.ws.jws2.AADisorderClient disorderClient;
+
+  public static jalview.gui.AlignFrame af = null;
+
+  @BeforeClass
+  public static void setUpBeforeClass() throws Exception
+  {
+
+    jalview.bin.Cache.initLogger();
+    disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
+    iupreds = new ArrayList<Jws2Instance>();
+    for (Jws2Instance svc : disc.getServices())
+    {
+      if (svc.getServiceTypeURI().toLowerCase().contains("iupredws"))
+      {
+        iupreds.add(svc);
+      }
+    }
+    assertTrue("Couldn't discover any IUPred services to use to test.",
+            iupreds.size() > 0);
+    jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
+    af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
+    assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
+  }
+
+  @AfterClass
+  public static void tearDownAfterClass() throws Exception
+  {
+    if (af != null)
+    {
+      af.setVisible(false);
+      af.dispose();
+    }
+  }
+
+  /**
+   * test for patches to JAL-1294
+   */
+  @Test
+  public void testDisorderAnnotExport()
+  {
+    disorderClient = new AADisorderClient(iupreds.get(0), af, null, null);
+    af.getViewport().getCalcManager().startWorker(disorderClient);
+    do
+    {
+      try
+      {
+        Thread.sleep(50);
+      } catch (InterruptedException x)
+      {
+      }
+      ;
+    } while (af.getViewport().getCalcManager().isWorking());
+    AlignmentI orig_alig = af.getViewport().getAlignment();
+    // NOTE: Consensus annotation row cannot be exported and reimported faithfully - so we remove them
+    List<AlignmentAnnotation> toremove = new ArrayList<AlignmentAnnotation>();
+    for (AlignmentAnnotation aa:orig_alig.getAlignmentAnnotation())
+    {
+      if (aa.autoCalculated)
+      {
+        toremove.add(aa);
+      }
+    }
+    for (AlignmentAnnotation aa:toremove)
+    {
+      orig_alig.deleteAnnotation(aa);
+    }
+    testAnnotationFileIO("Testing IUPred Annotation IO", orig_alig);
+
+  }
+
+  public static void testAnnotationFileIO(String testname, AlignmentI al)
+  {
+    try
+    {
+      String aligfileout = new FormatAdapter().formatSequences("PFAM",
+              al.getSequencesArray());
+      String anfileout = new AnnotationFile().printAnnotations(
+              al.getAlignmentAnnotation(), al.getGroups(),
+              al.getProperties());
+      assertTrue(
+              "Test "
+                      + testname
+                      + "\nAlignment annotation file was not regenerated. Null string",
+              anfileout != null);
+      assertTrue(
+              "Test "
+                      + testname
+                      + "\nAlignment annotation file was not regenerated. Empty string",
+              anfileout.length() > "JALVIEW_ANNOTATION".length());
+
+      System.out.println("Output annotation file:\n" + anfileout
+              + "\n<<EOF\n");
+
+      AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
+              FormatAdapter.PASTE, "PFAM");
+      assertTrue(
+              "Test "
+                      + testname
+                      + "\nregenerated annotation file did not annotate alignment.",
+              new AnnotationFile().readAnnotationFile(al_new, anfileout,
+                      FormatAdapter.PASTE));
+
+      // test for consistency in io
+      StockholmFileTest.testAlignmentEquivalence(al, al_new);
+      return;
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    fail("Test "
+            + testname
+            + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
+  }
+
+}

diff --git a/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java b/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
new file mode 100644 (file)
index 0000000..f7d0e48
--- /dev/null
+++ b/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
@@ -0,0 +1,64 @@
+package jalview.ws.jabaws;
+
+import static org.junit.Assert.*;
+import jalview.ws.jws2.Jws2Discoverer;
+
+import java.util.Vector;
+
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+public class JalviewJabawsTestUtils
+{
+  
+  @BeforeClass
+  public static void setUpBeforeClass() throws Exception
+  {
+  }
+
+  @AfterClass
+  public static void tearDownAfterClass() throws Exception
+  {
+  }
+
+  /**
+   * test servers
+   */
+  public static String[] serviceUrls = new String[]
+  { "http://localhost:8080/jabaws" };
+
+  @Test
+  public void testAnnotExport()
+  {
+    fail("Not yet implemented");
+  }
+
+  public static jalview.ws.jws2.Jws2Discoverer getJabawsDiscoverer() {
+    jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
+            .getDiscoverer();
+    int p = 0;
+    String svcurls="";
+    Vector<String> services = new Vector<String>();
+    for (String url : JalviewJabawsTestUtils.serviceUrls)
+    {
+      svcurls+=url+"; ";
+      services.add(url);
+    }
+    ;
+    Jws2Discoverer.setServiceUrls(services);
+  
+    try
+    {
+      disc.run();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+      fail("Aborting. Problem discovering services. Tried "+svcurls);
+    }
+    assertTrue("Failed to discover any services at ",
+            disc.getServices().size() > 0);
+    return disc;
+  }
+
+}