From 1cca7d8fe617a8a1587bc325bdce2d922f818445 Mon Sep 17 00:00:00 2001 From: Mateusz Warowny Date: Thu, 19 Sep 2019 14:35:46 +0100 Subject: [PATCH] JAL-3066 Auto discover multiple sequence alignment services --- j11lib/slivka-client.jar | Bin 114641 -> 116952 bytes src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java | 81 ++++++++++++----------- 2 files changed, 41 insertions(+), 40 deletions(-) diff --git a/j11lib/slivka-client.jar b/j11lib/slivka-client.jar index 9efae32cf535d615e9f6232be655ffd7d193a832..12cc028bf8119347640aa2c26be81e228d7ae786 100644 GIT binary patch delta 9907 zcmbVS34B!5)jwypH<`SIEM$WKlMupWvav5AtRX-kB&Jw2w5W%`71TqO>v$eKrUE8`<`9un$pVqzBR>}9jZ<5S}rS0#_FEjVPd(S=FJ@?#m z&YQPdEbr}5!lq0znmUu!YNg7`{&iskLT!^P`WKgcaO?Lrvlh9T^Xs>VjtmKxgN{pg z-?396+Np@zXB=YN6jieyVT(u{5>juE`BSJ7K=nV`XGiGJeLMHQIM+-x*R0j1vg4tV z98$ln?>LJN_3q&J!XqWl$6g!6edCDaXRx+n68F+x-@=`uvr5Zd)zzC<;>;F-Bo$6YO!HQywygt zX^uiA;+&c)M)kCX&7~WelvS?smG0t2V%~ybT0|s=W-!fD$xQQ^Opdg<1#+27rG-=q z;L55pPlc>NcP{=Lj&+jFQhNuIqw3x|U?po+Bw~`0M%iPtaRi5QFp2`X<-OOaI za<5qFsdAUuD4v$7R6&*EwaLAmD}c4ky~wq)yhhGct5idkz`w**EuUAZbPKI!vMhFs z@S^UPwREdO>$JVm9BZ9Rw=u;!3Iq@DoM@yq5GJEH0uXYX)fK*6yq2x zzIi!1%}P6%RM5;{U0S}f+Ox_n@d}k5pa+?3mCI|!R92R|T@~U?zt|pg(&ku6lM7s{ zgBEP2U6RR1#5cva@T0myw@nEjvxoL6w3jI|u)D3uBomKI!RMqEUNt$)M!V^NMEHbw zK4uD}eiHlLOKXYb5OMERJ0GlncB+j#V>2z~?ux}VOKjAgnpDc9*zV4q%~UyH)&{X?7SMM>|sObf--)Lvr!_Gr;( zYN&W^`hzhqhY-{2(wr>Pj^0%1EqYtrGGl~yHvLJZKhsOt{xQYHh54h4LICitO7F=r zOWuUyg1me=^npr$(ZR;%=M_vIT`0#sQt7N5GmR@K)PX)$>6{K!P&6ZdeEu{EbY7*u z>OeE{XU|aRB2$-uy6Oka+`?YVdj9T76RlBH@-dWj5YYvf# zol&>TQLh|EFEG5m4H%uaQ6FurZKlotC5bJKv^9uCD}}&lFa>X5c)PKIb~>XTl8uiZ z2EpC`CBgDWdQ1}Z(SEEt_#aoPx+c=)60bArP@BN$vr|L=D#h}XNw5uWDV!eSD7cGwdYHS@E>59G*h#y2 z6voHW9-aW_P(=H927JLB+RqE<09Vr!d^a8By_i2hhxrga#m~~OxSpQoCVGZXW9&Ed zJikJ<{5I9G_dPnopP=(MI?CVDG5!ZN@MZEDOw?$wQInw?9XBM=Q9~~}2`S~(qaPL; 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+ } + } + continue; + } + SlivkaWSInstance instance = new SlivkaWSInstance(client, service); + JMenuItem defaultEntry = new JMenuItem(String.format("%s with defaults", service.label)); + defaultEntry.addActionListener((ActionEvent evt) -> { AlignmentView msa = alignFrame.gatherSequencesForAlignment(); - if (msa != null) - { - new MsaWSClient(instance, alignFrame.getTitle(), msa, false, true, + if (msa != null) { + new MsaWSClient( + instance, alignFrame.getTitle(), msa, false, true, alignFrame.getViewport().getAlignment().getDataset(), - alignFrame); + alignFrame + ); } }); - submenu.add(defaultMenuItem); - - JMenuItem customMenuItem = new JMenuItem( - String.format("%s with custom parameters", names[i])); - customMenuItem.addActionListener((ActionEvent e) -> { + categoryMenu.add(defaultEntry); + + JMenuItem customEntry = new JMenuItem(String.format("%s with custom parameters", service.label)); + customEntry.addActionListener((ActionEvent evt) -> { AlignmentView msa = alignFrame.gatherSequencesForAlignment(); - if (msa != null) - { + if (msa != null) { try { - SlivkaParamSet paramSet = new SlivkaParamSet( - instance.getService()); - new MsaWSClient(instance, paramSet, null, true, - alignFrame.getTitle(), msa, false, true, - alignFrame.getViewport().getAlignment().getDataset(), - alignFrame); - } catch (IOException e1) + SlivkaParamSet paramSet = new SlivkaParamSet(service); + new MsaWSClient( + instance, paramSet, null, true, alignFrame.getTitle(), msa, false, true, + alignFrame.getViewport().getAlignment().getDataset(), alignFrame); + } catch (IOException exc) { - throw new IOError(e1); + throw new IOError(exc); } - } }); - submenu.add(customMenuItem); - } catch (IOException e) - { - // TODO Auto-generated catch block - e.printStackTrace(); + categoryMenu.add(customEntry); + + categoryMenu.addSeparator(); } + } catch (IOException e) + { + // TODO Auto-generated catch block + e.printStackTrace(); } - - wsmenu.add(submenu); } @Override -- 1.7.10.2