Merge branch 'develop' into releases/Release_2_11_2_Branch

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 1b4156e..3308456 100755 (executable)
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -90,10 +90,10 @@
                        <tocitem text="ClustalX" target="colours.clustal" />
                        <tocitem text="Zappo" target="colours.zappo" />
                        <tocitem text="Taylor" target="colours.taylor" />
-                       <tocitem text="gecos:flower" target="colours.gecos-flower" />
-                       <tocitem text="gecos:blossom" target="colours.gecos-blossom" />
-                       <tocitem text="gecos:sunset" target="colours.gecos-sunset" />
-                       <tocitem text="gecos:ocean" target="colours.gecos-ocean" />
+                       <tocitem text="gecos Flower" target="colours.gecos-flower" />
+                       <tocitem text="gecos Blossom" target="colours.gecos-blossom" />
+                       <tocitem text="gecos Sunset" target="colours.gecos-sunset" />
+                       <tocitem text="gecos Ocean" target="colours.gecos-ocean" />
                        <tocitem text="Hydrophobicity" target="colours.hydro" />
                        <tocitem text="Helix propensity" target="colours.helix" />
                        <tocitem text="Strand propensity" target="colours.strand" />

diff --git a/help/help/html/colourSchemes/index.html b/help/help/html/colourSchemes/index.html
index 672910e..e006618 100755 (executable)
--- a/help/help/html/colourSchemes/index.html
+++ b/help/help/html/colourSchemes/index.html
@@ -198,7 +198,7 @@ td {
                                                        <td></td>
                                                </tr>
                                                <tr>
-                                                       <td>gecos:flower</td>
+                                                       <td>gecos Flower</td>
 
                                                        <td bgcolor="#b18a51"></td>
                                                        <td bgcolor="#83bff1"></td>
@@ -225,7 +225,7 @@ td {
                                                        <td></td>
                                                </tr>
                                                <tr>
-                                                       <td>gecos:blossom</td>
+                                                       <td>gecos Blossom</td>
                                                        <td bgcolor="#8bc4b4"></td>
                                                        <td bgcolor="#fc9502"></td>
                                                        <td bgcolor="#b5c206"></td>
@@ -251,7 +251,7 @@ td {
                                                        <td></td>
                                                </tr>
                                                <tr>
-                                                       <td>gecos:sunset</td>
+                                                       <td>gecos Sunset</td>
                                                        <td bgcolor="#fea0fd"></td>
                                                        <td bgcolor="#85746a"></td>
                                                        <td bgcolor="#abc8f5"></td>
@@ -277,7 +277,7 @@ td {
                                                        <td></td>
                                                </tr>
                                                <tr>
-                                                       <td>gecos:ocean</td>
+                                                       <td>gecos Ocean</td>
                                                        <td bgcolor="#c6ca9b"></td>
                                                        <td bgcolor="#0ca0a8"></td>
                                                        <td bgcolor="#0adfc3"></td>

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 26c907c..316c1aa 100644 (file)
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -56,7 +56,7 @@ abstract public class Pfam extends Xfam
   /**
    * docs are http://www.ebi.ac.uk/interpro/api/
    */
-  private static final String DEFAULT_PFAM_BASEURL = "www.ebi.ac.uk/interpro/api/entry/pfam/$PFAMID$/?annotation=alignment:$ALTYPE";
+  private static final String DEFAULT_PFAM_BASEURL = "https://www.ebi.ac.uk/interpro/api/entry/pfam/$PFAMID$/?annotation=alignment:$ALTYPE$";
 
   static
   {