From: tcofoegbu Date: Tue, 2 Jun 2015 14:11:50 +0000 (+0100) Subject: JAL-1641 applet build fix X-Git-Tag: Release_2_10_0~646^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ddeb701f639a19574ad9caf87c2db74e4c4dd786;p=jalview.git JAL-1641 applet build fix --- diff --git a/.classpath b/.classpath index b7c26a4..0abfdb3 100644 --- a/.classpath +++ b/.classpath @@ -58,7 +58,6 @@ - @@ -66,5 +65,6 @@ + diff --git a/build.xml b/build.xml index 49fd37e..273c9e0 100755 --- a/build.xml +++ b/build.xml @@ -111,6 +111,9 @@ + + + @@ -165,6 +168,10 @@ + + + + diff --git a/lib/java-json.jar b/lib/java-json.jar new file mode 100755 index 0000000..2f211e3 Binary files /dev/null and b/lib/java-json.jar differ diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java index d507362..75e99a6 100644 --- a/src/jalview/io/HtmlFile.java +++ b/src/jalview/io/HtmlFile.java @@ -1,6 +1,27 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ + package jalview.io; -import jalview.gui.AlignFrame; +import jalview.api.AlignViewControllerGuiI; import jalview.schemes.ColourSchemeI; import java.io.IOException; @@ -51,9 +72,9 @@ public class HtmlFile extends AlignFile String alignmentJsonString = content.val(); JSONFile jsonFile = new JSONFile().parse(alignmentJsonString); - seqs = jsonFile.seqs; - seqGroups = jsonFile.seqGroups; - annotations = jsonFile.annotations; + seqs = jsonFile.getSeqs(); + seqGroups = jsonFile.getSeqGroups(); + annotations = jsonFile.getAnnotations(); showSeqFeatures = jsonFile.isShowSeqFeatures(); colourScheme = jsonFile.getColourScheme(); } catch (Exception e) @@ -62,7 +83,7 @@ public class HtmlFile extends AlignFile } } - public void applySettingsToAlignFrame(AlignFrame af) + public void applySettingsToAlignFrame(AlignViewControllerGuiI af) { af.setShowSeqFeatures(isShowSeqFeatures()); af.changeColour(getColourScheme()); diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java index ff7deaf..30383f3 100644 --- a/src/jalview/io/JSONFile.java +++ b/src/jalview/io/JSONFile.java @@ -1,3 +1,24 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ + package jalview.io; import jalview.api.AlignViewControllerGuiI; @@ -129,10 +150,8 @@ public class JSONFile extends AlignFile if (jsonExportSettings.isExportJalviewSettings()) { - jalviewVersion = jalview.bin.Cache.getProperty("VERSION"); - webStartLaunchServletUrl = jalview.bin.Cache.getDefault( - "www.jalview.org", "http://www.jalview.org") - + "/services/launchApp"; + jalviewVersion = ""; + webStartLaunchServletUrl = "www.jalview.org/services/launchApp"; JalviewSettingsPojo jvSettings = new JalviewSettingsPojo(); jvSettings.setGlobalColorScheme(globalColorScheme); @@ -178,7 +197,7 @@ public class JSONFile extends AlignFile jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo); } } - com.json.JSONObject generatedJSon = new com.json.JSONObject( + org.json.JSONObject generatedJSon = new org.json.JSONObject( jsonAlignmentPojo); jsonOutput = generatedJSon.toString(); return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend", @@ -380,7 +399,7 @@ public class JSONFile extends AlignFile String desc = annot.get("description") == null ? null : annot .get("description").toString(); - char ss = annot.get("secondaryStructure") == null ? null + char ss = annot.get("secondaryStructure") == null ? ' ' : annot.get("secondaryStructure").toString().charAt(0); String displayChar = annot.get("displayCharacter").toString(); @@ -548,6 +567,11 @@ public class JSONFile extends AlignFile this.showSeqFeatures = showSeqFeatures; } + public Vector getAnnotations() + { + return annotations; + } + public class JSONExportSettings { private boolean exportSequence; diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java index f40b302..67ab3f2 100644 --- a/src/jalview/ws/dbsources/PDBRestClient.java +++ b/src/jalview/ws/dbsources/PDBRestClient.java @@ -21,7 +21,7 @@ import com.sun.jersey.api.client.ClientResponse; import com.sun.jersey.api.client.WebResource; import com.sun.jersey.api.client.config.ClientConfig; import com.sun.jersey.api.client.config.DefaultClientConfig; -import com.sun.jersey.api.json.JSONConfiguration; + /** * A rest client for querying the Search endpoing of the PDB REST API @@ -49,8 +49,6 @@ public class PDBRestClient try { ClientConfig clientConfig = new DefaultClientConfig(); - clientConfig.getFeatures().put( - JSONConfiguration.FEATURE_POJO_MAPPING, Boolean.TRUE); Client client = Client.create(clientConfig); String wantedFields = getPDBDocFieldsAsCommaDelimitedString(pdbRestRequest