From 5a9c3ec689d94311666f7b3a26b192b5cc865b65 Mon Sep 17 00:00:00 2001 From: Jim Robinson <933148+jrobinso@users.noreply.github.com> Date: Tue, 10 Sep 2024 16:20:27 -0700 Subject: [PATCH] Add basemod colors for 3 chebi codes. See #1563 (#1566) --- src/main/java/org/broad/igv/prefs/Constants.java | 6 +++++- .../java/org/broad/igv/sam/mods/BaseModificationColors.java | 4 ++++ src/main/resources/org/broad/igv/prefs/preferences.tab | 3 +++ 3 files changed, 12 insertions(+), 1 deletion(-) diff --git a/src/main/java/org/broad/igv/prefs/Constants.java b/src/main/java/org/broad/igv/prefs/Constants.java index aa93e9656f..b8bc1a425f 100644 --- a/src/main/java/org/broad/igv/prefs/Constants.java +++ b/src/main/java/org/broad/igv/prefs/Constants.java @@ -197,6 +197,9 @@ private Constants() { public static final String BASEMOD_B_COLOR = "BASEMOD.B_COLOR"; public static final String BASEMOD_A_COLOR = "BASEMOD.A_COLOR"; public static final String BASEMOD_O_COLOR = "BASEMOD.O_COLOR"; + public static final String BASEMOD_17082_COLOR = "BASEMOD.17082_COLOR"; + public static final String BASEMOD_17596_COLOR = "BASEMOD.17596_COLOR"; + public static final String BASEMOD_21839_COLOR = "BASEMOD.21839_COLOR"; public static final String BASEMOD_OTHER_COLOR = "BASEMOD.OTHER_COLOR"; public static final String BASEMOD_NONE_A_COLOR = "BASEMOD.NONE_A_COLOR"; @@ -204,6 +207,8 @@ private Constants() { public static final String BASEMOD_NONE_T_COLOR = "BASEMOD.NONE_T_COLOR"; public static final String BASEMOD_NONE_G_COLOR = "BASEMOD.NONE_G_COLOR"; public static final String BASEMOD_NONE_N_COLOR = "BASEMOD.NONE_N_COLOR"; + + public static final String BASEMOD_GROUP_BY_STRAND = "BASEMOD.GROUP_BY_STRAND"; public static final String BASEMOD_SKIPPED_BASES = "BASEMOD.SKIPPED_BASES"; public static final String SMRT_KINETICS_SHOW_OPTIONS = "SMRT_KINETICS.SHOW_OPTIONS"; @@ -300,7 +305,6 @@ private Constants() { public static final String CIRC_VIEW_HOST = "CIRC_VIEW_HOST"; - /** * List of keys that affect the alignments loaded. This list is used to trigger a reload, if required. * Not all alignment preferences need trigger a reload, this is a subset. diff --git a/src/main/java/org/broad/igv/sam/mods/BaseModificationColors.java b/src/main/java/org/broad/igv/sam/mods/BaseModificationColors.java index a96874caea..f8c05e78b4 100644 --- a/src/main/java/org/broad/igv/sam/mods/BaseModificationColors.java +++ b/src/main/java/org/broad/igv/sam/mods/BaseModificationColors.java @@ -43,6 +43,10 @@ public static void updateColors() { colors.put("e", preferences.getAsColor(BASEMOD_E_COLOR)); colors.put("b", preferences.getAsColor(BASEMOD_B_COLOR)); colors.put("a", preferences.getAsColor(BASEMOD_A_COLOR)); + colors.put("17082", preferences.getAsColor(BASEMOD_17082_COLOR)); + colors.put("17596", preferences.getAsColor(BASEMOD_17596_COLOR)); + colors.put("21839", preferences.getAsColor(BASEMOD_21839_COLOR)); + colors.put("other", preferences.getAsColor(BASEMOD_OTHER_COLOR)); colors.put("NONE_A", preferences.getAsColor(BASEMOD_NONE_A_COLOR)); colors.put("NONE_C", preferences.getAsColor(BASEMOD_NONE_C_COLOR)); diff --git a/src/main/resources/org/broad/igv/prefs/preferences.tab b/src/main/resources/org/broad/igv/prefs/preferences.tab index e58cd6e1f5..9d7944d8b2 100644 --- a/src/main/resources/org/broad/igv/prefs/preferences.tab +++ b/src/main/resources/org/broad/igv/prefs/preferences.tab @@ -236,6 +236,9 @@ BASEMOD.E_COLOR 5fU color 141,221,208 BASEMOD.B_COLOR 5caU color 0,100,47 BASEMOD.A_COLOR 6mA color 51,0,111 BASEMOD.O_COLOR 8oxoG color 111,78,129 +BASEMOD.17082_COLOR pseU color 51,153,255 +BASEMOD.17596_COLOR inosine color 102,153,0 +BASEMOD.21839_COLOR 4mC color 153,0,153 BASEMOD.OTHER_COLOR Other color 132,178,158 ## Unomdified base colors (2-color option)